One of the things I used to do (and haven't in a while) is to reboot the machine into Linux (though with NTFS, some Windows-based boot CD would probably work better), create a new C:\OLDWIN directory, move everything into there, then install Windows. It won't notice that there's already a version of Windows installed, so you get a clean install, and you don't have to delete anything. Just make sure you don't let the Windows installer format your hard drive. Then once it's installed, you can move data back as you see fit.