Quite a bit actually. The PCV is the latest greatest. The biggest difference is that the PCV can use the auto tune kit to manage your fuel mapping. The PCIII has to have maps programmed into. So unless you are very confident in what you are doing you have to get the maps from a place like SLP, DynoTech, etc (or you will burn down your motor!). Also the PCV is smaller and uses a different file format for maps (so PCV maps are not directly compatible with PCIII maps). Here is a link. It's worth checking out their products.
DynoJet Power Commander