PCI-Express is a high-bandwidth, serial interface version of PCI. It has none of the special features of AGP, which many feel were never that special to begin with. Still, I've personally seen cards with identical GPU specifications where the AGP version outperformed the PCI-Express version by around 1-3 frames per second.
PCI-Express x16 is used for most graphics cards and has around twice the output bandwidth of AGP8x. But today's cards don't need that much bandwidth, hence there's no gain yet. It's a future-looking specification that will probably make for noticeable performance gains in a few years, but by then high-end AGP cards will be off the market.