teps for upgrading to Panther with the least problems:

1. If you have an external FW800 hard disk, check for firmware updates and apply them (e.g. LaCie: http://www.lacie.com/support/drivers ). 
2. Use one of the many utilities available to clean caches and run maintenance scripts. Utilities like MacJanitor, Jaguar Cache Cleaner, Cocktail, Onyx, etc. can be used (all available at versiontracker.com.) 
3. Boot from your Jaguar or Panther Installer Disk 1. After the installer loads select Disk Utility from the Installer menu. After DU loads select your OS X volume, click on First Aid tab, click on Repair Disk. If Repair Disk reports any errors that it cannot fix, you will need to use Drive 10 or Disk Warrior to repair the drive. Do not proceed until you have completely repaired the drive. If DU reports the drive is OK quit DU and the installer and restart. If you own Disk Warrior, it is a good idea to repair the drive/volume with it even though Disk Utility reports the drive is OK. 
4. Create a bootable backup of your hard disk to another drive/partition or an external drive using Carbon Copy Cloner (versiontracker.com.) 
5. Update any haxies (e.g. ASM, TinkerTool) or third-party preference panes, startupitems, and login items or disable/remove them. Also disable/remove any utilities that install in the menubar. 
6. Deactivate StuffIt AVR (StuffItDeluxe only), anti-virus programs, and other background programs. 
7. Disable/remove all Norton Utilities/Systemworks files. 
8. Power off any external firewire drives. Do not use a FW800 drive with Panther until you have installed a firmware update for it and updated Panther to 10.3.1. 
9. Unplug all other peripherals except your mouse and keyboard. 
10. Startup from the Panther Installer Disk 1 and proceed to install Panther. Use the Upgrade option. 
11. After restart load Disk Utility and repair permissions.