Well, thats the whole point of reformatting. Reformatting a media means to wipe it clean and start over. I think it might be a little easier for to to start clean, reinstall the OS on C and then immediately create a partition on D that houses ALL other programs, utilities, games, files, etc. THis way, you would leave the system partition a lot cleaner than what you are used to. Every once in a while, you could wipe just the D partition clean.
Out of curiousity.....why are you reformatting so much?