If you re-install Windows over the old version you already have it shouldn't affect the software you already have on the system. You DO have to go back to MS and re-install all the patches and updates etc. Thats about the only real headache. (Since MS stuff likes to be patched one at a time to get the best results that is a time thing). Just make sure you go right over the existing windows copy. (A new drive or directory installation WILL disconnect your other software)
But 99.9% of the time, no probs happen with the other progs. This system has had a reinstallation once every 6-8 months for 2 yrs now. Haven't lost one program yet.

But if you have data files from something really important like Quicken etc, you want to be safe and floppy backup for that. JIC!