For the most part, PCIe cards tend to have higher clock speeds than their AGP counterparts, but that's about it. The AGP card should fare pretty well against it's PCIe brother.
This kinda makes me mad, I bought a x800gt 2 weeks ago because they didnt have the x800gto in stock, but sure enough 3 days after I bought this one they got like 10 gto's, 10 gto2's, and dropped the price on everything. The list goes on and on.
I guess that's our downfall though, everything we buy gets outdated quickly and we have to upgrade upgrade upgrade. The computer industry really has a choke-hold on us eh?
Sry for the thread hi-jack btw
EDIT: My post is just assuming you have two of the same cards, not comparing the 7800gs and gt. Although if the 7800gs/gt relationship is anything like the 6800gs/gt relationship, the gs could give a gt a run for it's money when OC'ed and unlocked if possible. But then of course you could also OC the gt. Never ends, lol.