My Windows 7 problem

So I was playing Modern Warfare 2 when I went to go get the phone. Nobody else is in my house and my screen was untouched. I noticed no sound was playing when I got back so I quit the program and checked all my speaker connections, everything checked out. I try playing multiple songs on FooBar 2000 and the program would just crash. I restarted my machine and booted into Windows 7 and my sound was back, however when I clicked on any application Icon, it said the link was broken.

When trying to start it by executing the .exe in the application's folder (stored on another partition), the application simply crashes when I try to do anything, and if it's a portable application (StepMania), it says it can't find application files.

I did a system restore and it fixed nothing. In Linux (Ubuntu 9.10), I can run everything perfectly so this is an OS problem. How do I fix this without reformatting?

EDIT: If nobody knows how to fix this or it's pretty much not worth fixing, does anybody know how to get my registry to add entries to already installed programs? I don't want to have to fiddle with settings for my speaker driver and games every time I boot into Windows.

Have you tried a system restore to a previous point in time to see if this helps??

I did a system restore back 2 months ago when I last made any changes on my machine. Nothing. I may just reinstall anyways considering it would be good to back up my registry after installing applications and restoring it before those instillations so I can fix these problems.

EDIT: If nobody knows how to fix this or it's pretty much not worth fixing, does anybody know how to get my registry to add entries to already installed programs? I don't want to have to fiddle with settings for my speaker driver and games every time I boot into Windows.