Jen Edwards, AKA Pocket Goddess, has a nice, brief procedure for doing a clean-sweep re-installation on a Palm OS device. This might be worth storing somewhere, for the time you buy a new device and need to transfer data, or just want to start from scratch. Thanks Jen!
For Mac OS X users the advice is similar, except that your files are going to be found in a directory similar to this:
Hard Drive/Users/mrohde/Documents/Palm/Users/Mike Rohde/
I'll usually copy and rename the 'Backups' directory inside of the Palm/Users/Mike Rohde/ directory along with a backup of the 'User Data' file used by Palm Desktop.
To be extra safe, I'll backup the device onto the SD card using BackupMan ($10 shareware). For quick restores, where the machine is working fine, I'd just use BackupMan to restore the device rather than going through the whole clean restore procedure.
For data transfers from Palm OS 2, 3 or 4 to Palm OS 5 (or shortly, OS 6), it's a good idea to start as much from scratch with all applications as possible. Make sure they're the latest versions, compatible with your machine's OS. This includes anything other than standard stuff like Address, Datebook, To-Dos and Memos. Why? Well, some old apps could really hose up your new machine. I know, because it happened to me. :-)
Hope that's helpful!