Busto, if I'm reading you right, it sounds like some of these corrupt files are Windows system files.
1. If they're program files, uninstall and reinstall the offending programs.
2. If they're Windows files, then you need to do procedures to verify and restore system integrity.
A. Run checkdisk (if you haven't).
B. There are some shorcuts for scanning and restoring Windows sytem files including (1) reinstall OutlookExpress/Internet Explorer with an upgrade (this replaces many integral system files), (2) reinstall or upgrade your Service Pack, and (3) there're a dos command that causes Windows to scan the installation disc and replace any divergent files -- I haven't got this command in front of me, but there are references to it on these boards.
C. Get a program like Registry First Aid, Registry Healer, or Norton WinDoctor to verify registry extensions. This will not fix corrupted files but it may fix broken links in the registry to files that no longer exist.
Other people here will have other terrific suggestions. You might also do a careful search of these forums for links on repairing windows. Good luck.