If you are using win XP, the operating system files reside in the windows folder & documents & settings folder which contains users information. Program files folder contains all the files and information about the programs you are using, both the programs which were installed with windows installation and programs that you have installed by your own.
I think you will need to backup everything other than those folders, along with the My Documents Folder, the outlook file if you are using outlook for your email, and any other folder you use that contain information you need.
Don't try to backup program files. If you are going to install a new copy of windows, you will have to install all the programs once again from scratch as you did before.
Thanks,