It takes all of a day to reinstall. If you don't reformat, you can usually "repair" an installation, or do an update without losing your installed programs.
Grab your windows disc. If you don't have one, get one through any means necessary. Follow this:
http://support.microsoft.com/kb/929833It should be able to restore missing files.
Finally, common sense rules that microsoft seems to not beat into people:
Turn off "hide extensions for known file types" so that you don't run an exe. If you ever download anything off of the internet which has the exe or bat file extension, scan it first with an antivirus, unless you are certain it is safe (downloaded off majorgeeks.com or from the official site. Some common sense should be applied here which I can't teach).
Stop using Safari and/or IE. Both have serious exploits available in them which the parent company tends to hide before they fix, rather than announcing it. Try SRWIron/Chrome, Opera, or Firefox. Firefox is quite popular, which decreases its safety by obscurity which macs are steadily losing. If you use firefox, I suggest you install noscript and get to know it well. It will block all obtrusive ads unless you allow them, and it won't block simple ads (so make sure you click them!). Noscript will block almost everything that makes the web advanced (videos, music, flash) unless you specifically allow it. It breaks an awful lot of sites, but it also means that nothing will run without you wanting it to, meaning any sort of flash or java exploit available in the browser will not run. It's extremely useful for sketchy sites.
System restore doesn't work. Anti-Virus programs don't work. The only viruses which can do serious damage are the ones you run some exe for, which Anti-Viruses can't stop. They may detect the virus, but any decent virus will be rootkitted and recreate itself after it is deleted, or the file will be "in use" so you can't delete it. While an alternative OS will be able to delete said files, there is no way to be certain you deleted them all, and your system will be forever compromised until you reformat and reinstall.
"Parliamentary inquiry, Mr. Chairman - do we have to call the Gentleman a gentleman if he's not one?"