Currently no card even utilizes PCI-E so a 6800GT PCI-E and 6800GT AGP are basically the same.......as I've come to find out however....the Nf3 chipset (for AGP cards) seems to be a little lacking in stability for cards....meaning my 430/1150 6800GT OC worked fine on my XP-M system but since going AMD64, it seems my limit is around 420/1125.....any more than that and it'll cause 3dmark03 to freeze during a test for a few seconds.....this is all thanks to the chipset although I'm still trying a few things to see if I can get past this, or atleast get closer to my original overclock.
However, even with a lower overclock, going to an AMD64 system that is 600MHz slower in terms of clock speed + the card being not OC'd as high still yields 300points more in 3dmark03 than before....that tells you right there your card runs better on the AMD64s