make sure you create an export of your registry files....
I've done exactly what you are doing now. I had windows installed on the C: drive, games, applications on the d: drive.
After I formated and installed windows, many of the installed software programs on the other drive no longer worked in windows due to the registries not being right. As a result, I had to delete those programs and reinstall them.
I believe that if you make a copy of your original registry file, and import that file into your new windows install, all your previously installed software will still work.
Course, if your registry is the reason why your redoing windows, this doesn't help you much....
Have fun...