With Leopard and prior versions of OS X, one of the popular maintenance utilities was AppleJack, which is a free SourceForge project and ran in the Terminal (preferably Single User mode) as an easy-to-access way to run a bout of cleaning functions on the Mac. AppleJack so far has been incompatible with Snow Leopard, but with today's update the Snow Leopard incompatibility has been squashed.
Troubleshooting Tools: AppleJack
Whither AppleJack? UPDATE: Intel-based version available
AppleJack 1.4.3 final edition released; Intel-based Mac compatibility
Utilities Updates: Impression 2.7; AppleJack 18.104.22.168; iTattle 1.5; System Optimizer X 4.6.1; more
Utilities Updates: AppleJack; NAV defs; FireFox; UltraPointer; Screen Query; Synchronize! Pro X; MailArchive; Uninstaller
Utilities Updates: AppleJack 1.4.2; Google Maps Plugin (Universal Binary) 2.3; Ghost Sphere 1.2.4; more
"WebDAV File System Authentication" box persistently appears, does not accept password
There are many times when in our articles we will mention "General Maintenance" as part of a troubleshooting routine. If you are having software issues, either with third-party applications or the Mac OS itself, giving the computer a virtual scrub-down will many times help, or at least give you a cleaner slate upon which to do more in-depth troubleshooting.
There are a variety of tools available for managing your hard drive's structure and data. Most are shareware utilities that give you function or time limits until you register the program, but there are a few out there that are both useful and free.