AGP will be HD 4650 I think you will have the budget to obtain the AGP version (AGP versions are more expensive than their counter parts) PCI express then also 4650 or 4670. Any thing else will bottleneck the system.
Most 939 systems had PCIe. There were a few AGP systems but they weren't common. Fx-60 was a good chip in its day, but that day has past. You could probably get away with something a bit more then the 4670, but I wouldn't bother with anything faster then the GTS250/5750/4850. Knowing the budget, games you play, resolution, etc would help in this decision. As would knowing if that FX-60 is OC'd.
The max cards I recommend would be HD4850 or GTS250. There is no reason to go for HD5750 and DX11 compatibility unless you are running Windows Vista or 7.
AGP was the graphics interface before the PCI express replace it.