if you want to "future-proof" your computer, PCIe will be the way to go. AGP will in time become like the PCI and the PCI will become like the ISA cards. basically the new technology is rolling in. and the new "out-dated" technology i being rolled out, as new and faster hardware and peripherals come out. it is a bit more Xpensive, but you will get more life out of your board and PC now rather than buying an AGP board now then few years later buying a PCIe board, better to go now then later and be spending more money on the board and the peripherals and possibly a new case depending on the FormFactor of the MoBo.
hope this is helpful
hope this is helpful