What are your concerns with upgrading? Do you need to upgrade for any particular reason?
I for one, wouldn't even consider upgrading any MS operating system. Just personal preference with years of experiences to back it up. And if you did....I would take advantage of NTFS and move away from FAT. Without NTFS, a lot of the win2k functionality is lost. If you do upgrade, the registry and the file system should remain intact though....to answer your question.