Square one

If you use windows, I recommend using the Windows Live One Care... It cleans your registry, history, scans for viruses, and will fix any issues you might have. The whole scan takes about 4-5 hours, but it's really worth it in the end.
http://onecare.live.com/site/en-us/default.htm
go here and click the full service scan button.
it will download the necessary tools, and you can choose to start the scan then or do it later

Replying to #21

I want a system where if a file is missing, it doesn't sit there and bitch about it missing.
Instead, it recreates the file (matching OS version, service pack etc.) and proceeds as normal.
Deleted your graphic driver? No problem, restart, fix, done.