It will depend on how you have everything intsalled.
Everytime I've re-installed windows I've formatted the hard drive, so if you have your data stored on that same drive then you will need to back it up.
Also, any programs that are intsalled into the windows registry will need to be re-installed. Maybe there are some tricks to backing up your registry and then copying it over to the new computer, but that seems pretty sketchy to me.
I'm not aware of a way to easily re-install only windows without affecting other programs, but I am by no means an expert.
Definitely back up any important data before you do anything drastic.
-D'oh!