the difference is the bandwidth, from 8x on agp to 16x on pcie. Also, the voltage, most entry level gfx cards don't need extra power from the PSU on the pcie socket where it needed one on the AGP. If your mobo only supports the PCIe socket, it's not compatible with AGP, physically and if you do manage to put it on - it wont work. So say goodbye to the AGP socket.
OH you edited it! I would go for the Inno 3D, simply because it's cheaper and the XFX adds more RAM which was not needed and it's Ram is only DDR2 whereas the Ram on the inno 3d is DDR3. My only con for the Inno 3d is that I've never heard of it, but that's not an issue here.