format and re-install windows, but i'm assuming you're trying to avoid that. It's tough to say, most programs (including those listed in many places on this site - which noting your activity you've probably seen) if they are unsure, will leave a registry key, if a key that is needed is removed the program associated with it may not work.
What kind of programs are you trying to install and what exactly is the problem (eg: nothign happens, wrong installer runs, program has old values?)
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