Unreal Tournament user details, from name, to video and sound options, to skins, are all stored in the .ini files you see sitting in the base UT folder. Keep these files stored away when you delete the rest of the stuff, and drop them back into the freshly installed UT folder when you are done. This should preserve all of your user preferences. I'm not sure about the actual application preferences file itself, but if you want to be sure, then back it up as well, and if you need it, then drop it back into the preferences folder (or just keep it there; if you aren't having any problems with the game so far then there's no real reason to get rid of it at all).
Blizzard.