You could rem out pretty much everything in your autoexec and config.sys files and boot straight to a DOS prompt without loading Windows. If you hit F8 after your keyboard initializes but before the Windows logo screen pops up, it'll give you a menu; I think option 6 is "Command prompt". You might be able to run the DOS version of Scandisk from there even if you can't run it from Windows, since win.com and whatnot won't be sitting resident in the background, like they are if you start a DOS prompt from Windows. I don't really know though. I've never had a virus either. I guess it could be a virus. Trying to boot from a floppy is also a good idea, like other people mentioned.

If all else fails, you could always format your drives.