I'd assume that unless you delete the partition(s) during the re-install of the os, you'll be ok just formatting the partition. I don't know if your games and such will still work after reinstalling windows - there'd be some registry problems there surely?
I have two hard-drives - C for OS and programs. E for data/files. Makes life easier as you can backup all critical data before the old windows mantra 'format, reinstall'
