When I was in networking school I got the best tip ever. The guy who taught me this actually wrote a bunch of the drivers for Unix for the military in the late 60's and 70's. Now he does multi-media.
Start from scratch always. Run windows on its own partition. If you use 4 gigs for XP & 2k that would be plenty. Set another partition up and intall all of your programs on that. The final partition will be for all your files and/or downloads.
This is for a few reasons.
Windows should hardly ever need to be defragged. It works alone!
If a program you install skrews with anything, it will only skrew with other programs. Windows should be fine.
If you download or get a virus, it might corrupt your files, but windows will be intact as well as your programs. Personally, my hard drive have 5 partitions. I download into a smaller one and once I am sure there is no virus, then I move it over. I also have DOS on a very small partition (C:). Hackers and Viruses look for C: sometimes.
Windows rarely crashes for me. Every once and awhile I have a program crash, but I don't have to reboot.
I hope this helps everyone