Kappy's Personal Suggestions for OS X Maintenance
For disk repairs use Disk Utility. For situations DU cannot handle the best third-party utilities are: Disk Warrior; DW only fixes problems with the disk directory, but most disk problems are caused by directory corruption; Disk Warrior 4.x is now Intel Mac compatible. Drive Genius provides additional tools not found in Disk Warrior. Versions 1.5.1 and later are Intel Mac compatible.
OS X performs certain maintenance functions that are scheduled to occur on a daily, weekly, or monthly period. The maintenance scripts run in the early AM only if the computer is turned on 24/7 (no sleep.) If this isn't the case, then an excellent solution is to download and install a shareware utility such as Macaroni, JAW PseudoAnacron, or Anacron that will automate the maintenance activity regardless of whether the computer is turned off or asleep. Dependence upon third-party utilities to run the periodic maintenance scripts was significantly reduced since Tiger. These utilities have limited or no functionality with Snow Leopard or Lion and should not be installed.
OS X automatically defragments files less than 20 MBs in size, so unless you have a disk full of very large files there's little need for defragmenting the hard drive. As for virus protection there are few if any such animals affecting OS X. You can protect the computer easily using the freeware Open Source virus protection software ClamXAV. Personally I would avoid most commercial anti-virus software because of their potential for causing problems. For more about malware see Macintosh Virus Guide.
I would also recommend downloading a utility such as Lion Cache Cleaner, TinkerTool System, OnyX, or Cocktail that you can use for periodic maintenance such as removing old log files and archives, clearing caches, etc.
For emergency repairs install the freeware utility Applejack. If you cannot start up in OS X, you may be able to start in single-user mode from which you can run Applejack to do a whole set of repair and maintenance routines from the command line. Note that AppleJack 1.5 is required for Leopard. AppleJack 1.6 is compatible with Snow Leopard. There is no confirmation that this version also works with Lion.
When you install any new system software or updates be sure to repair the hard drive and permissions beforehand. I also recommend booting into safe mode before doing system software updates.
Get an external Firewire drive at least equal in size to the internal hard drive and make (and maintain) a bootable clone/backup. You can make a bootable clone using the Restore option of Disk Utility. You can also make and maintain clones with good backup software. My personal recommendations are (order is not significant):
Carbon Copy Cloner
Data Backup
Deja Vu
SuperDuper!
SyncTwoFolders
Synk Pro
Synk Standard
Tri-Backup
Visit The XLab FAQs and read the FAQs on maintenance, optimization, virus protection, and backup and restore.
Additional suggestions will be found in Mac Maintenance Quick Assist.
Referenced software can be found at CNet Downloads or MacUpdate.
Be sure you have an adequate amount of RAM installed for the number of applications you run concurrently. Be sure you leave a minimum of 10% of the hard drive's capacity as free space.
