I agree with Bateluer.
The Cards are based on the same reference card the NV 43, with 8 pipes and 3 vertexs, both work on a 128 bit bus.
heres a link to the different arcitecture designs of most cards
cards
The difference is the Core speeds and the Mem difference. The core on the 6600 is 300. The core on the GT is 500.
The mem DDR1 is only 500mhz on the non-gt. On the gt they have the much faster DDR3 at 1000 mhz.
Thats a huge speed difference and will make a huge difference when trying to scale games up, and turn on all the pretty details.
Not sure this is any thing to "mod" from a 6600 to a GT, your not going to be able to change the mem, or increase the core from 300-500. So i would say NO on the modding.. it just doesn't make any since.
The other 2 points are this.
The NON-GT is PCI Express only. Do you have a newer PCI-e motherboard? If not the 6600GT is your only choice, becuase it comes in an AGP.
Also, if you do have a PCI-E motherboard, you should be picking the 6600GT hands down. The 6600 NON-GT is not SLI. The 6600GT is. So down the road you will be able to hook up 2 6600GT's together.
So i guess im saying.. you should pick the GT hands down. If you do have a pci-e mobo, you should be picking the GT, and if you dont, then the GT is your only choice anyways.
As for benchies... from what I have seen, the GT offers a 25%-40% upgrade becuase of the DDR3 ram, and the faster clock.
Hope this helps!
Chris