Just the other night I cleaned out my 800MHz TiBook.
1. Tidied up all the documentsand schtuff.
2. installed the latest OS upgrades
3. repaired permissions
4. ran OnyX
5. repaired permissions again
6. rebooted zapping the P-RAM
7. cloned the system disk onto an external drive using Carbon Copy Cloner
8. booted from the external drive and erased the laptops internal drive
9. cloned the system back on (the net result of 7. 8. and 9. is a complete defrag).
There is a marked difference. Instead of the drive grumbling for about a minute after log on it is now silent instantly. If you are looking for good tools for OSX definitely check out the above.