Some further research has shown up this page.
This lists all supported hardware (ATI is O.K) and the fact there is a console version which isn't listed on the Folding@home download page. You will almost certainly need to update your drivers for GPU3 to run properly. Follow the links to get the console version, I'd advise you use the console version as all you need to do is complete your current unit, using the -oneunit flag, then unzip the files into your GPU2 directory and restart.
EDIT..Some more info...Installed GPU3 console version on an Nvidia 9600GT, picked up a GPU3 unit, a whopping 1300 pointer, ppd similar to GPU2.