AGP over PCI---AGP. PCIe over AGP? No, PCIe.
PCI: 32-bit, 33MHz bus (where the total bandwith is shared between all devices using the bus), equalling 133MB/s peak transfer rate.
AGP: 32-bit, 66MHz (at AGP 1x, multiply 66MHz by AGP tranfer speed), running at 266MHz, with a single device (i.e. an AGP video card) on it's bus. AGP is simply a specialty higher-clocked PCI slot.
PCIe (PCI Express, denoted as either PCIe or PCI-E, do not use PCI-X---it's a different interface) is a serial (point-to-point, no sharing) technology, consisting of lanes coming from the chipset. Each lane runs at 500MB/s, and is to replace the PCI bus. PCIe slots are labled x1, x2, x4, and x16, which state the number of lanes going to the PCIe slot. The shortest PCIe slots are x1, while x16 slots are the longest.