Mostly I learned on 3DS Max. I did a bit of Maya as well. I learned all the basic texturing programs, but Photoshop dominates the rest. I loved After Effects. I spent more time making my videos in there than I did modelling and animating them.
I was required to learn other stuff like AutoCAD and Rhino, but I didn't get into technical drawings so they don't come into play much.
EDIT: I never used After Effects after school. It turned out not to be very practical for me.