I'd have to agree with SiN. Installing programs will add registry entries to your Windows installation. These will need to be replaced when you do a fresh install of Windows. The only real effective way of doing that is reinstalling each and every program.
(NOTE: it is possible but completely inadvisable to backup your registry and copy it over the fresh one)
The ghost option is a real good suggestion for future reinstalls. But that's an entirely different subject so please ask if you need more info on that.
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