It depends how you reinstall the system. If you do a REPAIR installation in the same directory, it will keep all applications.
However, if your application has been damaged, the repair reinstalltion doesn't help to recover it.
The best way it: put all user date on drive D:;install a clean OS and all applications on drive C:; then make a ghost image (use Norton Ghost) on either drive D: or DVD rom. Whenever there is a problem or you need a clean system, recover the whole syste (both OS and applications) from the ghost image.