Windows 7 had native QuickTime codecs that probably will not work b/c of your installation of QuickTime.
The easiest way would probably be to run
to get your system back to the original status - but since you have installed so much, it might be (theoretically) easier if you started out from scratch.
iTunes had issues in the past, cannot remember what, but I have never used it at all. I have
installed the Seven Codecs and the 64bit codecs from shark007.net to get my stuff playing - since it now supports native captions in MKV format in WMC, I don't bother with anything else.
See SFC /SCANNOW Command - System File Checker
for an extensive tutorial on SFC.
This has the potential to break many things that rely on modified system files, hence my suggestion to start all over again.