If your running Win2000 or XP, Just put the CD in and 'fix a damaged installation.' It reinstalls all system files to their original versions.
That replaces the system files, but keeps most of your registry intact, so as not to damage installed software. I tried that a few times, and not only didn't it fix anything, but I ended up with several duplicates of my Documents and Settings folder, with no reliable way to get rid of them.
If spyware or other software you don't trust has corrupted your system, you might as well just re-install... and give your family another big lecture on installing crap. I ususally don't have to re-install my families' computers, though. I've never heard of a background task or config change that automatically closes windows. IE, in particular, will throw a fit if you try to close a window with JavaScript (even though you can OPEN as many as you like!)
I miss the non-registry days. Programs didn't care if they were installed or not, they just ran wherever you put them! You may not have to re-insall programs, since they rebuild their registry data as needed. Only programs with passwords and stuff may throw a tantrum.
