At the current time, there is no difference between PCI-E and AGP8x Graphics cards but in the future PCI-E cards will be far superior to AGP8x... the slot itself, PCI-E Is much better...
BTW, as far as current SLI technology goes, I think both cards share the load @ 8x8, future technology will be 16x16. On low resolutions you will not notice that large of a difference using SLI, however, on high resolutions the difference is HUGE.