I think Maya is the de facto standard for animation and modeling in graphics. Since I'm mostly doing graphics programming right now, I use OpenGL, which is a programming interface for C++. It's pretty low-level stuff, so mostly i end up importing models and animating small parts of them, so far.
I think you have a good point, Martin, but I think you could take it a little further. Admittedly, you do have an advantage if you are specialized, but it also helps a lot to be able to quickly pick up new subjects: often the desired specialists of the moment change, and that might be kind of harsh if your specialty falls out of style. A broad base helps that. I'm not actually even normally allowed to specialize yet - I just find it silly that I should wait until my last year of undergraduate studies to really get involved in what I want to do.