This is how i set mine up, if i only have one drive i partition it in 2, one for my system and one form my games and docuemtns and all the stuff i dotn wan to loose so that when i need to reinstall i jsut format the first partition (system) and reinstall windows on the first partion and the second partition stays in tact.
Now with your issue, alot of the porgrams you have installed in your add/remove require regestry keys which go when you re-install windows. So if you format you first partition with windows, your programs go to. You will ahve to re-install all the programs you had installed, it can be annoying. Lucky with me, mainly all my big programs are games and I can usually get away with out haveing to re-install them as there are reg fixes and some dont require acutall regestry keys.
Office and things liek that require regestry keys.
Hope that helps