After Effects CS6 has a built in motion tracker and some performance changes. It also has built in 3d renderer, but its very limited and takes a lot of resources. Don't get CS6 if you don't plan on using that stuff.
After Effects CC (newest) Cinema4d integration, mask tracker, and smaller improvements.
It doesn't really matter which version you get, you'll mostly be doing the same stuff. Don't go below CS4 though, most plugins and effects are outdated or don't work.