AGP is pretty much going cold now, it was the industry standard for a long time, up to about the release of the ATI X800 series, up till then it was mainly AGP. PCI-e works on a serial bus which greatly reduces interferance, whereas PCI and AGP work on a parralell bus, AGP connects directly to the memory and the northbridge for fast data transfer. There was also a standard "VESA" but it was god-awful becuase it connected DIRECTLY to the FSB of the proessor, and with the connector producing interferance, you couldn't touch or move the computer without it rebooting.
So PCI-e is the standard now, you will rarely see a motherboard being sold thats got AGP unless its a very bottom end board.
Ruan