Well, there isn’t much to go on, since there were no Apps when the OS 2.0 upgrade was released. The more recent smaller upgrades haven’t even reorganized my Apps.
At worst, when you upgrade you will have a clean hard drive, and then the Restore option will be offered to add your Contacts, Calendar, Music, Email, and Applications as they were on your previous backup – so Sync the iPhone immediately prior to performing the upgrade. iTunes has a list of all the Apps you’ve purchased, so even if you need to start from scratch, it’s as simple as checkng the Apps you want on the iPhone in iTunes and Syncing, then arranging the icons where you like them.