Highly recommend "Archive and Install"
Gives you a clean system folder .... everything else left untouched ..
Apple - Archive and Install
http://docs.info.apple.com/article.html?artnum=107120
Before Installing
1. Backup valuable data
2. Boot from the Panther "Mac OS X Install CD 1" go to upper left of screen to "Installer" menu in order to open the "Disk Utility". Then, click on "First Aid" and repair the hard drive. Then Repair Permissions.
If you wanted to be super careful you could run Disk Warrior if you have it ..
Unplug all your peripherals except your mouse and keyboard before installing
Also ....
After updating to Panther and after any update .. Repair permissions: Close all files and applications on the disk you want to repair. Go to Applications/Utilities/Disk Utility and double click it. Then select your hard drive in the left panel and First Aid at the top. Then click on "Repair Permissions." It will take a few minutes.
Here is a document that goes into more detail about installs in general, and the options if you choose to customize ... very well written.
Panther Installation Process
http://discussions.info.apple.com/We...f1.0@.599b3b48
Good luck ... You will love Panther!