Slow operation and generally unusual behavior are signs that may indicate that permissions need to be repaired on your Macintosh's hard drive. To do so you can run Repair Disk Permissions from within Disk Utility, located on your hard drive at: Applications/Utilities/Disk Utility

Note: There is no need to verify permissions before you repair them. Unless you can read the report and understand what Disk Utility proposes to do, there is little point in verifying first.

For some reason permissions often seem to get fouled up under OS X 10.2. Under OS X 10.3 through OS X 10.6, file permissions are less of a problem. But you should still run Repair Disk Permissions regularly. Maybe once a month, and every time after you have installed new software.  (Contrary to popular belief, it is not at all necessary to run Repair Disk Permissions prior to installing new software.  Though doing so won’t hurt anything.)

Open Disk Utility, and on the left side of the screen select your hard drive, then select the First Aid tab on the right side and click on "Repair Disk Permissions."

See:
http://docs.info.apple.com/article.html?artnum=106712
and
http://support.apple.com/kb/HT2963
for further details.

Note: Some users are reporting that they run Repair Permissions over and over again, and the same permissions are reported as being incorrect, and they are not being repaired. You should know that, in addition to reporting faulty permissions, until very recent versions of OS X, running Repair Permissions in Disk Utility also gave you advisory messages. For instance, it might report that it is using an updated set of rules to determine if any permissions needs to be repaired. These are not error reports and they will not change no matter how many times you run Repair Permissions. Advisory messages do not indicate that anything is wrong, and they can safely be ignored. Example:

"We are using special permissions for the file or directory
./System/Library/Filesystems/hfs.fs/hfs.util.
New permissions are 33261"
http://docs.info.apple.com/article.html?artnum=107298
As of OS X 10.4.6, Repair Permissions no longer gives these advisory messages.
http://docs.info.apple.com/article.html?artnum=303411

Note: With OS X 10.5 (Leopard) a number of problems were introduced for some users when trying to repair permissions.  Early versions of Leopard had a problem whereby running Repair Disk Permissions might take a long time and you might get a lot of SUID or ACL error messages. For most, but unfortunately not all, users, this can be remedied by updating to the latest version of Leopard or updating to Snow Leopard (OS X 10.6). (For those for which updating does not help, sometimes downloading and running the latest updater again helps.)

About "ACL found but not expected" or “Warning: SUID file” error messages
http://docs.info.apple.com/article.html?artnum=306925
These messages can safely be ignored.

"Permissions nightmare with Leopard (10.5)”
http://forums.macosxhints.com/showthread.php?t=80606

Note: Some users have noted that their permissions revert to apparently incorrect settings every time that they restart their Macintosh.  Disk Utility/Repair Disk will correct their permissions, but the next time that they restart the permissions have been changed again.  This has been traced to the fact that these users are running security software such as Intego’s Virus Barrier.  The security software is intentionally modifying permissions to close off potential malicious exploits.  Note that in this case, it is neither necessary, or even desirable, to repeatedly repair your permissions to “fix” this situation.

Discussion.

Maintenance Myth #1: "You need to repair permissions from a copy of Disk Utility that resides on the drive that you are repairing."
This is a myth that is very prevalent.

It used to be that you were warned against repairing permissions on one disk while booted from another because only the receipt files on the drive you were booted from would be consulted, not the receipt files on the drive you were repairing, and thus not all permissions would be set correctly. Though it hasn't been documented by Apple, this is no longer necessary. As of late in OS X 10.2, you can run Repair Permissions while booted from a disk other than the one that you are repairing (e.g. the OS X installer CD-ROM), and it will correctly use the receipts on the disk being repaired.

From Macintouch (http://www.macintouch.com) on 2/18/06:

Dan Frakes (author of the excellent book Mac OS X Power Tools and a staff member of Macworld magazine), followed up on "repair permission" confusion:

David Marshall wrote, "Those who warn against repairing permissions on one disk while booted from another seem to be basing that warning on a mistaken premise...In fact, repairing permissions uses the receipts from the /Library/Receipts folder on the volume you're repairing permissions on, not the volume you're repairing them from."
This likely stems from the fact that in older versions of Mac OS X (pre-Jaguar, I believe), the Repair Permissions procedure did indeed use the /Library/Receipts folder on the boot volume, even if you were trying to fix an alternate volume. (This was even noted in Apple's support documentation. For example, if a permissions issue prevented you from booting off your normal boot volume, Apple recommended using the Repair Permissions function while booted from the Mac OS X Install disc and then, once you were able to successfully boot from your normal volume, use the procedure again to ensure the "correct" receipts were used.)

In Jaguar (again, as I recall), the procedure was changed -- without much documentation -- to use /Library/Receipts on the volume being repaired, boot or not. Unfortunately, many people who had become familiar with the original procedure never realized it had changed. 

See Mark Douma's Disk Utility post in the Apple Discussions User Tips Library for more info.
http://discussions.apple.com/thread.jspa?messageID=607431

Maintenance Myth #2: There are some folks who are very adamant that you never need to repair permissions under OS X. While repairing permissions isn't a panacea, they are wrong, it is definitely worth your while to repair permissions occasionally. The reality is that Repairing Permissions doesn't require that you purchase anything to do it, it can be accomplished fairly quickly, it doesn't hurt anything, and after repairing permissions sometimes the problem(s) that the user is experiencing are gone. In addition, often the curative effects of repairing permissions are repeatable and predictable. I don't see any reason not to do it.

Apple has been clear about the fact that repairing permissions is sometimes necessary, that you should do so routinely, and they have provided a tool to do so (Disk Utility/Repair Disk Permissions).
http://docs.info.apple.com/article.html?artnum=25751

It seems to me that Apple's engineers know best.

Apple offers a list of reasons why you may need to repair permissions
http://docs.info.apple.com/article.html?artnum=106712

Mac Help (the built-in help system that is part of OS X) tells you that repairing permissions should be done routinely.
http://docs.info.apple.com/article.html?path=DiskUtility/10.5/en/duh17.html

Here is a (rather extreme) example of the "it's never ever necessary" school of thought:

Exercises in Futility Part 2: Repairing Permissions is Useless
http://www.unsanity.org/archives/000410.php

From the folks at MacFixIt, who recommend routine repair of permissions:

Another follow-up to the Repair Permissions debate
http://www.macfixit.com/article.php?story=20060505112437423

The MacFixIt article makes this excellent point: While Disk Utility's Repair Permissions feature only repairs permissions for Apple Software (and not any third party software), much of that Apple software is system software, and that system software contains routines that are accessed and used (and used often) by third-party applications. Thus, incorrectly set permissions, contrary to what some would tell you, can cause problems with third-party applications.

These MacFixIt articles further explain what repairing permissions does, and they document real-world cases where repairing permissions was extremely helpful to users.:

Unraveling the Repair Disk Permissions controversy
http://www.macfixit.com/article.php?story=2006050407462364

Repair Permissions Success Stories
http://www.macfixit.com/article.php?story=20060728075547277

More Repair Permissions Success Stories
http://www.macfixit.com/article.php?story=20060731081527212

Dan Frakes has written an excellent article for Macworld on permissions and the need to repair them:
Repairing permissions: What you need to know
http://www.macworld.com/2006/08/secrets/repairpermissions/index.php

Microsoft Office, and especially Microsoft Word, often requires, and responds very well to repairing permissions:
http://word.mvps.org/Mac/DiskIssues.html

Return to Table Of Contents

OS X runs its own built-in maintenance routines, sometimes called "cron jobs", or "maintenance scripts", automatically between 3:00 am and 5:30 am each day. (There are daily, weekly and monthly scripts).
http://support.apple.com/kb/HT2319
The thing is that these scripts do just about nothing of great importance.  If they don't run for weeks, or even months, it's just not a big deal.  So, despite the fact that these are called "maintenance routines," don't get concerned if they haven't run in a long time.  Don't ignore doing this entirely, though, because in time failure to run the maintenance scripts will allow your Mac's hard drive to fill up with a bunch of invisible log files.

You can find a rundown of what the built-in maintenance routines do at:
http://arstechnica.com/civis/viewtopic.php?f=19&t=454874
http://discussions.apple.com/message.jspa?messageID=8906776#8906776

Prior to OS X 10.5, if you didn't leave your computer on 24 hours a day, or if you left it on but you let it go into sleep mode at night, these routines weren't run.   As of OS X 10.5 and later your Mac will run its maintenance scripts automatically at the next available opportunity if you put your Mac into sleep mode all night.  Though the scripts still won't run if you shut your Macintosh down at night.
http://discussions.apple.com/message.jspa?messageID=6552347
http://discussions.apple.com/thread.jspa?threadID=2143195&tstart=0
http://developer.apple.com/macosx/launchd.html
NOTE: As of OS X 10.5 the maintenance scritps are no longer handled by the UNIX facility "cron", they are now handled by a similar facility called "launchd," if that means anything to you.

If you are running OS X 10.2 you should probably run all the maintenance scripts manually every month or two if you shut your Mac down at night.
You can run these routines manually, whenever your want, with the free utility MacJanitor:
http://personalpages.tds.net/~brian_hill/macjanitor.html
NOTE: MacJanitor is not compaitlble with OS X 10.5 and beyond. For OS X 10.5 and beyond, if you decide that you want to run the maintenance scrips manually, you can instead use this free utility:
Maintidget
http://www.giantmike.com/widgets/Maintidget.html

If you are running OS X 10.3 to OS X 10.6, the easiest thing to do is to download and install the free utility PseudoAnacron which will make sure that your routine maintenance scripts run every time that you startup your Macintosh:
http://www.jaw.it/pages/en/x_misc.html
NOTE: On PseudoAnacron's Web site it says that it works with OS X 10.4 to OS X 10.5.  I've been in touch with PseudoAnacron's developer, and he says that it works perfectly with OS X 10.6 also.  There is an earlier version of PseudoAnacron available for OS X 10.3.

Discussion.

If you want to be sure that the built-in maintenance tasks have been run, the daily, weekly and monthly maintenance scripts each write the details of every run into their own log file, which you can check. Open the Console application (located at: Applications/Utilities/Console), go to:
File --> Open Quickly --> /var/logs/. Select "daily.out", "weekly.out" or "monthly.out" for the maintenance logs.

Return to Table Of Contents

Even though running the routine maintenance scripts clears out some temporary files, none of the system caches are touched by them. Occasionally caches become corrupted, impacting the performance and stability of your Mac.  So it is a good idea to every rare now and then use a utility that clears the system caches, and/or your Internet browser caches. Deleting caches won't hurt anything. However, over time a cache speeds up your computer (assuming that you do some things repetitively), so if you aren't experiencing any problems, you may want to leave your caches alone. On the other hand, if it has been ages since you have flushed your caches, or if your computer is running slowly, or if you are experiencing odd problems, it might be a good idea to flush them. Use your discretion.

Cache Out X is a free program which cleans out system and Internet browser caches. This can prevent some very hard to diagnose flaky behavior. (You may not want to regularly clear your browser cache if you have a slow speed connection to the Internet.  Until your browser cache is rebuilt, your access to favorite sites may be very slow.) You can get Cache Out X from:
http://www.trilateralsystems.com/CacheOutX/

According to MacAddict, October 2005, page 20, it is a good idea to occasionally clear out application-specific caches. They specifically recommend clearing out the two main cache folders in Mac OS X:

1) /Library/Caches, and 2)~/Library/Caches. ("~" stands for the folder with your username on it in your Users folder.) While Apple doesn't recommend doing this routinely, they indicate that it is a good idea in certain situations:
http://support.apple.com/kb/HT1199

 A MacOSXHints tip also suggests clearing out the application cache files occasionally:
http://www.macosxhints.com/article.php?story=20060111202501460

This hint notes that there may be quite a few extraneous cache files in your ~/Library/Caches folder.

You get to the ~/Library/Caches folder by following the path:
[hard drive] --> Users --> [your user name] --> Library --> Caches.

You get to the /Library/Caches folder by following this path:
[hard drive] --> Library --> Caches

You should be able to delete everything safely. However, if you want to be extra careful, just create a new folder on your desktop, and drag everything from your Caches folder into it and restart. You can trash the folder on your desktop when you are certain that everything is running fine.

Return to Table Of Contents

Preferences become corrupted way too often under OS X 10.2. This is still a problem under OS X 10.3, but much less of a problem under OS X 10.4 and later. If an application or applications quits unexpectedly under OS X, the first thing to suspect is that you have one or more corrupted user preferences files.

Preferential Treatment
http://www.jonn8.com/html/pt.html
is a free utility that will check for corrupted preferences files. (It will sometimes even locate preferences files that are corrupted before you start experiencing any problems from them, so it is a good idea to use Preferential Treatment regularly. About once a week.) Preferential Treatment allows you to delete any corrupted preferences files from right within the program, so that they will be rebuilt when you restart the effected applications.

Once all of your preferences files are known to be in good shape, it is a good idea to back them up.  That way, in the future if you have a problem with a corrupted preferences file, you can replace the corrupted file instantly with a clean copy. This also allows you to avoid having to re-set any application or system preferences settings.  You can use a backup program for this, or you can copy your entire Preferences folder manually.  You can find your user Preferences folder at:
~/Library/Preferences

You get to the ~/Library/Caches folder by following the path:
[hard drive] --> Users --> [your user name] --> Library --> Preferences

Make a copy of the user Preferences folder by holding down the Option key and click-dragging the folder to your desktop.  This will leave the original in place and make a copy on your desktop.  Click on the copy on your desktop once to select it, and choose File --> Create Archive.  This will compress the folder, making it inactive (so your Mac's system doesn't get confused by having a duplicate Preferences folder for any reason) and stash the duplicate folder somewhere where you can find it if you ever need it.  (Do NOT keep the duplicate anywhere in the Library folder.)

In the event of corruption of either individual preferences, or the entire folder, you can simply substitute the backed-up preference file, or the entire backed-up Preferences folder for the existing one. This eliminates the need to troubleshoot your user preferences if you suspect that one of your preferences files is corrupted.

If an application unexpectedly quits under OS X 10.4 or later, you are given the option of restarting that application with its ".plist" (preferences) file(s) deactivated, to see if that was the problem, and if it was, a new ".plist" is substituted for the old one. This approach isn't as pro-active as using Preferential Treatment routinely, but it should be entirely adequate and effective.

More information:
Tiger's new and improved “application crash” dialogs
http://www.macfixit.com/article.php?story=200505120750592

Preferences Files: The Complete Story (Part V); How .plist files become corrupt and troubleshooting the results
http://www.macfixit.com/article.php?story=20060606082246983

Return to Table Of Contents

I recommend that you occasionally restart your Mac, and hold down the Shift key right after the startup chime is played, and keep it held down until the spinning black bar cursor appears.  There is  no need to hold down the Shift key past the time that the spinning bar cursor appears.
http://support.apple.com/kb/HT1455?viewlocale=en_US
This procedure invokes what Apple calls a "Safe Boot":
http://support.apple.com/kb/TS1417
and your Mac will report that it has been booted (started up) into Safe Boot mode. During startup in Safe Boot mode your Mac will do a file system check, entirely in the background, with no working status indicated, or report generated, and any problems will automatically be repaired.
http://support.apple.com/kb/HT1564?viewlocale=en_US
It may take a while for your Mac to start up in Safe Boot mode. Be Patient.  Once it has fully started up, you should immediately restart your Mac normally, because certain files are deactivated when you startup in Safe Boot mode.

Note: A wireless or Bluetooth keyboard and mouse may not allow you to startup in Safe Boot mode.  (Also, be sure that all of the latest updates for your computer are installed.)
http://support.apple.com/kb/HT2220 
Item #6

Instead you may prefer to check your hard drive, and repair any problems, by using the method outlined below. The advantage of using the method outlined below is that both a working status indicator, and a report, are generated. The disadvantage is that you will have to have, and start up from, your OS X Installer CD-ROM.

Put your OS X Installer CD-ROM (or DVD) into your optical drive (if you have multiple installer disks, use the first one), and startup from it (by holding down the "C" key during startup or restart). From there you can choose Disk Utility from the Installer menu. Click on the disk that you want to repair in the left column and then choose the First Aid tab, and then click on Repair Disk. (If the Repair Disk button is gray, you either didn't click on the correct item in the left column, or you aren't started up from the Installer CD-ROM. You can't repair the disk that you have started up from.)
http://www.fixya.com/support/r935084-mac_repair_disk

Discussion.

Longtime Macintosh users know that under OS 8 and OS 9, if you were experiencing nasty problems with your hard drive, that running Apple's Disk First Aid usually didn't fix them. In such cases, users often resorted to using the commercial product Disk Warrior, which could perform near miraculous feats of repair on your hard drive. It was also an invaluable tool for routine preventative maintenance. Under OS X, Disk Utility/Repair Disk is the replacement for Disk First Aid. So, the question most folks have is, 'is Disk Utility/Repair Disk as lame as Disk First Aid, and is Disk Warrior still an invaluable utility to have?' There is an interesting thread on TidBits Talk that covers this topic:
Looking for Disk Warrior Justification
http://emperor.tidbits.com/webx?14@@.3c7926a4/

The answer is that Disk Warrior is a marvelous tool...when you need it. Fortunately, under OS X you don't need it as often as you needed it under previous versions of the Mac OS. For instance, you don't need to run Disk Warrior routinely as a preventative measure. (Though doing so, if you already own Disk Warrior, isn't a bad idea.) OS X is plenty stable without having to constantly rebuild its directory. And so, in my opinion, there is no need to purchase Disk Warrior (for about $100) unless a situation arises where Disk Utility/Repair Disk reports that it can't repair a problem with your hard drive. This is not to demean Disk Warrior. When you do need Disk Warrior, because your disk directory has developed errors that Disk Utility can't fix, it is a godsend to have.
http://www.alsoft.com/DiskWarrior/

For further information about disk repair software, have a look at:
http://db.tidbits.com/getbits.acgi?tbart=07451,
with a follow-up on TechTool Pro at:
http://db.tidbits.com/getbits.acgi?tbart=07696

There are other ways to run a file system check/Repair Disk under OS X, such as by booting into Single User Mode, or by running the command "fsck" from the Terminal, but these are more advanced ways to do exactly the same thing, that I don't think that the average user needs to know about.
For more information than you need, see:
http://support.apple.com/kb/TS1417

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Macintosh Myth #3: Most folks with an opinion will probably tell you that Mac's running OS X never need to have their hard drives defragmented.

Here is a quote from a MicroMat technician, that I think is very insightful:
The claim that installations of Mac OS X on HFS+ volumes do not fragment is a myth believed by people who do not have disk optimizers that allow them to see how much fragmentation their disks have. It is an example of ignorance that is not able to be removed by any amount of evidence. I think theologians call that "invincible ignorance". It is now a widespread form of the pollution of information space.
http://www.macfixitforums.com/ubbthreads.php/ubb/showflat/Number/570817/site_id
/1#import
or
http://tinyurl.com/yuqn4

Actually, Some Macs running OS X can benefit quite a bit from defragmenting their hard drive. But not for the reason that you might expect There is often little in the way of performance to be gained by defragmenting your hard drive. But defragmenting your drive can stave off some very flaky behavior, out of memory errors, and possibly even data loss.

OS X handles "file" fragmentation (a file being broken up into chunks and strewn across your hard disk) automatically, and fairly well, every time that you launch a fragmented file under 20MB.
http://article.gmane.org/gmane.comp.macosx.general/22906
http://arstechnica.infopop.net/OpenTopic/page?a=tpc&s
=50009562&f=8300945231&m=9900929295
(registration required to access)
http://forums.macrumors.com/archive/index.php/t-13383.html

But OS X doesn't handle "drive" fragmentation (small bits of free space between files) well at all. In fact, OS X is prone to huge amounts of drive fragmentation.

Drive (as opposed to file) fragmentation under OS X is mostly irrelevant with respect to performance, as long as it isn't severe. Where hard drive fragmentation becomes important is when there are no longer any large contiguous chunks of free space left on your drive for OS X to use for working space, for virtual memory, temp files, databases, etc. When this happens, OS X can start acting flaky, and eventually, in extreme cases, it will suffer from data loss.
http://www.macfixit.com/comment.php?mode=display&sid=20070301091515843
&title=Does+Mac+OS+X+need+a+disk+defragmenter%2Foptimizer
%3F&type=article&order=&pid=25346

I used to recommend that folks defragment their hard drive when it was approaching 80% full (no matter how large the drive is), because I've heard from so many folks who were experiencing out-of-memory errors and flaky behavior at this level (no matter how large their drive was), and defragmenting invariably fixes the problem. But I've heard from a number of users who made heavy use of their drive, and they have experienced the problem as early as around 60% full. And other folks won't experience the problem until their drive is well over 80% full. Clearly how you use your drive makes a difference as to when, or if you run out of free contiguous space on your hard drive.

So now, instead of using a rough rule of thumb on when you should consider defragmenting your hard drive, what I recommend is that folks check to see how much free contiguous space the is on their drive routinely, once their drive is over 50% full. You can do this quickly and easily with the free demo version of iDefrag:
http://www.coriolis-systems.com/iDefrag.php
or the free utility ShowVolumeFragmentation
http://www.macupdate.com/info.php/id/18451

There is no need to purchase anything until and unless you need to. When you have no large chunks of free contiguous space left, you can expect problems to begin to appear if you don't defragment your drive. Note that if you let this problem advance too far, it may become for any utility to work on your drive, protesting that there isn't enough free space on your drive for it to be able to run. (This despite the fact that you may have many gigabytes of "total" free space left on your drive.)

You may never need to defragment your drive (prior to purchasing a new one because the old one is becoming too full) or you may need to do so much earlier than you would expect, but by checking with one of these free tools you won't have to guess whether it is necessary or not.

If you drive needs to be defragmented, the "only" hard drive defragmentation utility that I recommend is iDefrag. (See my comments about other hard drive defragmentation utilities in Note 1. below) It is the only one that I know of that can optimize the files on your hard drive in a totally OS X-savvy way. OS X, under OS 10.4 and 10.5, has a journal, a hot band, virtual memory, metadata, etc. to keep track of. It is very important that these things be located properly on the disk or performance will be compromised.
Technical data about the hot band and meta data on hard drives running OS X 10.4 and later:
http://developer.apple.com/technotes/tn/tn1150.html#HotFile

iDefrag is the only hard drive optimization tool that does this perfectly (despite what some of the other companies that make hard drive defragmentation tools say).

The downside to iDefrag is that you can't do a comprehensive defrag without booting from a volume other than the one that you are defragmenting. Coriolis Systems offers free software to allow you to make a boot CD-ROM to run iDefrag from.
https://secure.coriolis-systems.com/login.php?targetPage=customer-licenses.php

Another option, instead of defragmenting your hard drive with a software utility program, is to simply purchase a new, bigger hard drive; copy all of the data on the old drive to the new drive, and then reinitialize (i.e. wipe clean) the old drive and start over with it. Moving all of your data from one drive to another will automatically defragment your data. Though it won't optimize it.

You have to reinitialize your data on the old drive for this plan to work, because if you just move "some" data from your old drive to your new drive, the old drive will still be badly fragmented, and without defragmenting the old drive it will still probably be flaky. (That is, even if you free up some space on the old drive, there more than likely still won't be the large chunk of contiguous free space available that the OS likes to run properly.)

Defragmenting your hard drive prevents any unusual behavior from your OS because it creates contiguous space, combining fragments of space strewn all over your drive into one large chunk of space.

Note that clearing off data from your drive, even a large amount of data, without also defragmenting, may not create enough "contiguous" space to keep your Mac running well.

Discussion.

Definition of Terms:
Types of fragmentation:
1) "File fragmentation, where file are broken up and are not contiguous
2) "Drive" fragmentation, where, though files may be contiguous, the free space on the drive is fragmented.

"Defragmentation" means that things (that is, data, e.g. files and applications, and free space) are made contiguous (that is, not broken up into small bits and strewn about at different places) on your hard drive.

"Optimization" means that not only is the drive defragmented, but data is put where it should be and.or is put where it will provide optimum performance.

Let's refer to files A, B, C and D, and free space "__".

Here is a drive with no file fragmentation. All the files are contiguous, but free space is fragmented. In other words, there is no file fragmentation but there is disk fragmentation:
AAAAA__BB__CCCCC__DDD_

Here is a drive with both the files and free space fragmented:
AA__BBA__CCCCCB__DDDAA_

Here is a drive with no file or free space (disk) fragmentation. All of the files are contiguous, and all of the free space is contiguous:
AAAAABBBCCCCCDDD__________

Now, take a look at that first example, where there is a lot of disk fragmentation even all of the files are contiguous. Have you ever run a Mac under OS X with too little RAM? It was a dog, wasn't it? That's because your Mac was hitting your disk in a big way, using virtual memory instead of RAM for tasks. Now, think of the effect that you might see if you forced your Mac to use hundreds of little spaces all over your drive to write virtual memory to, instead of having it written to one big contiguous space. That's why drive fragmentation is more important than file fragmentation.

OS X automatically defragments files. OS X doesn't do any drive defragmentation at all.

Note that if you actually defragment your hard drive as part of a routine maintenance program (rather than just keep track of how much free contiguous space is available), let's say every coupe of months, then it won't take long to defragment your drive each time, and any potential problem will never rear its head. In addition, you should be able to use close to every last gigabyte of space on your hard drive, and you will always have every last ounce of performance that your Mac can give you as as side benefit.

See Note #1 below for more information on file defragmentation.

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Hard drives are quite a bit more reliable these days than they were just a few years ago. Unfortunately, the old saying that "all hard drives die eventually" is still true. It would be nice to know in advance when a hard drive is going to fail. That way you would have time to backup your data before your drive ultimately met its end. S.M.A.R.T. (Self-Monitoring Analysis and Reporting Technology) is a feature built into most modern hard-drives that acts as an "early warning system" for pending drive problems. OS X 10.3 and above have this ability built-in, but it only works if the actual hard drive in your Mac has this technology built-in also. Disk Utility, which comes with OS X (it is in your Application/Utilities folder), under OS X 10.3 and above can tell you the S.M.A.R.T.-status of your hard-drive. Unfortunately, you have to remember to regularly launch Disk Utility to check this. (See below for free utilities that will automate this process.)

To check your drive's S.M.A.R.T.-status using Disk Utility, launch Disk Utility and select your hard drive. If at the bottom of the window it says "Verified," your drive is in good shape. If it says: "About To Fail" you need to:
1) Not shut down your computer and hard drive until you have done the following...
2) Back up your hard drive, which you should do immediately, if you haven't already done so.
Hard drives on their last legs often will finally fail by refusing to start up.

I've been told that there is no hope for an internal drive once it reports "Failing" as its S.M.A.R.T status. Its time to get a new drive.

SMARTReporter is a free application that can automatically warn you of hard-drive failures before they actually happen! It does so by periodically polling the S.M.A.R.T.-status of your hard-drives.
http://www.corecode.at/smartreporter/

SMARTer is a free utility that reads mounted disks' S.M.A.R.T. status and reports it. You add it to your Mac's login items to have it run regularly.
http://www.euronet.nl/~tekelenb/software/index.html

Volitans' SMART Utility ($20 for a 10 copy license) is different from other similar utilities which only read the overall S.M.A.R.T. Status. SMART Utility goes farther and displays the individual attributes tracked by S.M.A.R.T in an easy to read format so that you can see their status and information, and it also uses its own internal algorithm based on those attributes to detect drives failing before S.M.A.R.T. normally would. This pre-fail detection can save your data well before S.M.A.R.T. has determined that the drive is failing.
http://www.volitans-software.com/Home.html

Note: FireWire and USB hard drives (that is, external hard drives), even if their internal mechanism is S.M.A.R.T.-enabled, can't be checked for S.M.A.R.T. status.

Discussion.

There was a study released by Google:
http://research.google.com/pubs/papers.html
http://research.google.com/archive/disk_failures.pdf
Failure Trends in a Large Disk Drive Population, which concluded that S.M.A.R.T. wasn't a reliable predictor of drive failure.

More information on S.M.A.R.T. technology:
http://www.ariolic.com/activesmart/smart-technology.html
http://support.apple.com/kb/TA27350
http://www.storagereview.com/guide2000/ref/hdd/perf/qual/featuresSMART.htmlhttp://en.wikipedia.org/wiki/Self-Monitoring%2C_Analysis_and_Reporting_Technology

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Moving things to a location other than on your desktop is an easy and free way to pick up better performance. Users have noticed that reducing the number of items on their Mac’s desktop can noticeably increase the performance of certain activities in OS X. This is easy to do. You can even create one folder on your desktop and put everything on your desktop in it. That will do the trick. Nested items within folders on the Desktop don't count. It is only the total number of items directly on your desktop that matter.
http://www.macosxhints.com/article.php?story=20051117154624368

http://www.macworld.com/2006/03/features/speedtoptips/index.php

Another way to go is to put all of the items that would normally reside on your desktop, that you want to be able to access quickly, in a folder; park that folder somewhere other than on your desktop, and then drag that folder to your Dock so that it is always available from the Dock. Whenever you click and hold (or Control-click, or right-click on a two button mouse) on that folder in the Dock, you will be presented with a menu of everything in that folder to choose from. Sort of like the old classic Apple Menu.
Under OS X 10.5 this problem is ameliorated because your Mac’s desktop is no longer the default location for new downloads.  There is a separate Downloads folder in your Dock.

Discussion.

Things that you put on your desktop don't really reside there. They actually reside in a folder in your user account. The Desktop folder can be found at:
[hard drive icon]/Users/[your user name]/Desktop
otherwise known as: ~/Desktop, or your user desktop folder.
Open this folder and you will find everything that you see on your desktop!

It would be logical to conclude that the things represented on your desktop use a good chunk of cached memory and/or that it is CPU intensive to draw the icons for the things that reside on your desktop. And to a certain extent this is true, because under OS X each icon on your desktop is more like a folder than an ordinary icon.  However, I’m told that another source of the slowdown from keeping an excessive number of items on the Desktop is due to the “windowserver” process generating a huge number of logfiles, which draws resources away from other system tasks.

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Lots of folks have problems with Safari bogging down and/or exhibiting the spinning beachball. When this starts to be a problem, there are several things that you can do to fix this.

This hint from MacFixIt, http://www.macfixit.com/, works really well for some:
"… go to /(username)/Library/Safari folder and delete the Icons folder."
This will clear cached favicons (little icons that appear in the address bar).

This tip from Mac OS X Hints will keep this folder from filling up with favicons again:
http://forums.macosxhints.com/archive/index.php/t-36615.html

From MacFixIt:

Under Mac OS X 10.3.x and Mac OS X 10.4.x there exists and issue where some users experience a stall in Safari or other Web browsers when accessing certain Web sites that usually leads to a complete system freeze accompanied by the unending "spinning beach ball" process indicator.

One solution to this problem is the free utility Unlockupd:

http://www.dshadow.com/software/unlockupd/

A rather extreme, but simple and usually quite effective thing to do is to restore Safari to like-new performance is to reset Safari, which will clear Safari's cache and other gunk:
Choose "Reset Safari" from the Safari menu and click "Reset".

Note. Resetting Safari clears the history, empties the cache, clears the Downloads window and removes all cookies. It also removes any saved user names and passwords or other AutoFill data and clears Google search entries. I'm also told that resetting Safari alters your keychain and bookmarks. For this reason you may want to make copies of the files:
~/Library?Cookies/
~Library/Keychains/
and
~/Library/Safari/
so that those can be restored after resetting Safari.

As of Safari 3.0 the "Reset Safari" command has been substantially improved, now offering users the option to customize the "reset", and "delete only select items". It also now has the capability to remove all Web site icons ("favicons"), which can have a surprisingly dramatic performance boosting effect for Safari.

Discussion.

There are lots of great hints for Safari maintenance here:
http://www.macoxshints.com/article.php?story=
20040324004506941&query=safari%2Bspeed

Safari performance tips from MacFixIt:
http://www.macfixit.com/article.php?story=20070416000657464

Safari performance tips from MacRumors:
http://guides.macrumors.com/Speed_up_Safari

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Sometimes, under OS X 10.4, your Macintosh will slow to a crawl, and you can hear that there is a lot of hard drive activity, even though you aren't doing anything disk-intensive with your Mac. To determine what's running in the background, start up Activity Monitor (in Applications/Utilities folder), set it to show "All Processes" and sort by down-arrow "% CPU". That'll show which processes are running, and which, if any, are hogging CPU cycles to the point of drastically slowing down your Macintosh. Look for Dashboard widgets that are hogging CPU cycles. Poorly coded widgets have been known to hog CPU cycles even when you would expect them to be inactive. Uninstall any CPU hogging widgets.

If the culprit is something named "mds" or "mdimport" (the processes that handle Spotlight data), it could signal corruption of your Spotlight database. (Make sure that you aren't just seeing normal Spotlight indexing. See if this problem perseveres after your computer has been left on all day.) If this problem persists, you can easily rebuild your Spotlight database by opening System Preferences, choose the Spotlight panel, click on the Privacy tab, and drag your main drive's icon into the Privacy window. Now highlight your hard drive's icon within the Privacy window and

click on the "-" button (that is, the minus button in the Privacy Window).

Or you could highlight the hard drive icon in the Privacy window and hit the delete key. This will cause the Spotlight database to be deleted and automatically rebuilt. (You won't be able to use Spotlight while its database is being rebuilt.).

After doing this, leave your Mac on for an entire day (making sure to set the Energy Saver System Preferences so that your Mac won’t go to sleep) and allow Spotlight to index your entire drive uninterrupted.

Some have suggested that it might be a good idea to rebuild your Spotlight database after every time that you update to a new version of OS X (a full "point" release, e.g. 10.3 to 10.4) .

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As of OS X 10.4, all archived messages in Apple’s Mail program are kept in individual Finder-readable files. There are no archived messages in Mail's database.  OS X keeps your archived mail messages in this folder: ~/Library/Mail/Mailboxes/

This is a good thing.  Some other e-mail programs, notably Microsoft’s Entourage, store all of your messages in one big monolithic database.  If the database in a program with a monolithic database becomes corrupted and unrepairable, you can lose all of your archived mail.

However, Mail’s performance can lag, and it can become less stable, as you store more and more archived messages in it:

http://support.apple.com/kb/TS1895?viewlocale=en_US

Periodically deleting old, unwanted e-mail messages, and rebuilding Mail’s database, will usually give Mail a very noticeable performance boost, and help ensure continued trouble-free operation.

Since there are no archived e-mail messages stored in Mail’s database, it is quite safe to rebuild Mail’s database, because if something goes wrong with the rebuild, you can just start over, having lost nothing.

Every now and then (or, ideally, routinely as you use Mail) you should go through all of your mailboxes in Mail and delete all of the messages you no longer wish to keep. Then, in Mail, choose:
Mailbox menu --> Erase Deleted Messages --> In All Accounts to purge all deleted messages.

After doing this, quit Mail.

You can then use this free utility to quickly and easily rebuild Mail's database:

SpeedMail (free, donations accepted)
http://www.1802.it/speedmail.php

Or, instead, you can use this program, which has the advantage that you can set it to run automatically on a schedule:

VacuumMail (free)
http://www.musingsfrommars.org/2007/04/vacuummail-will-speed-up-apple-mail.html

For many folks, storing their old e-mail messages, and being able to search through them, is very important.  Unfortunately, if you use Mail itself to store huge amounts of archived e-mail, eventually doing so will impact both Mail's performance and stability.  There are a number of automated backup/archive utilities for Mail, listed on the following Web site, that will allow you to both backup and search through archived mail outside of Mail itself:
http://www.hawkwings.net/plugins.htm#archive
I've been asked if just backing up all the folders in:

~/Library/Mail/Mailboxes/

does a sufficient job of backing up one's e-mail.  I've heard from a number of users who have had to restore their e-mail from backups of this type, and they have reported problems getting Mail to integrate and recognize individual messages when they have had to restore them from such a backup. Most of the application-specific Mail backup programs claim to instantly do that for you. Which sounds like a nice feature to have.  (Of course, as of OS X 10.5, you can just use Time Machine to back up and access archived e-mail messages.)

Discussion.
For background on what SpeedMail does, see:

http://www.hawkwings.net/2007/03/01/a-faster-way-to-speed-up-mailapp/
http://www.hawkwings.net/2007/03/03/scripts-to-automate-the-mailapp-envelope-speed-trick/

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