A lot of games with work fine, although when trying to run patches on them -after a OS reinstall- you might hit problems as the patches usually check the registry for location, version etc, so they might give you errors about not being able to find the game. A few will then still allow you to point to the folder and patch up ok (often putting the relevant registry entries in along the way), others just wont patch without the registry entries. You could find the releveant registry entries and restore them but tbh unless someone thinks up some automated way of doing this, it's probably less hassle to just reinstall the games.
One thing I do for my main game, RTCW, is use winzip to copy the files like config, custom maps etc (savegames for SP games), so i have a "rtcwbackup.zip". Then when i reinstall i just patch up then unzip backup zip in the rtcw folder - make sure it uses folder names and everything will be back where it should be. Similar with IE favourites, custom taskbar menu's etc... many things can simply be added to one big zip and done at once (remember to save full folder path for this though). I guess somewhere there's some files storing my XP tweaks etc, but I dont know of them
Any app that doesnt require registry can be backed up in full (e.g. mirc/nnscript etc); for any that cant, backup the settings files etc <- just either remember to install apps to the same path, using the defaults & maybe changing drive letter helps.
Another benefit of having most things on seperate drive is you can do the above even after a partition format + OS reinstall, should things go really bad
I guess thats simplar to ghosting or other backup, but i find that method simple, if a little time consuming, and very easy to extract only the files etc that you want.
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