If your motherboard has an AGP slot, use it, buy the AGP. AGP is much faster than PCI, because its tuned for a graphics card.
Most AGP(Accelerated Graphics Port) ports are accelerated, and run much faster than PCI Slots.
PCI slots run slower, and are a generic slot for various boards (NIC, Sound, modem, ect). Thus they share bandwidth on a PCI bus, which means other devices must share the same bus.