There are some options in 3D as TrueSpace and others. 2D seems to have less tools.
Anyway, a Lab Pack for 3D Studio Max, a very expensive tool, is around 4500,00 for 25 machines. Almost the price of one professional license. They do this to help the growth of his product. That's why I asked.
I don't know if they control the use but what the license give us is a 25 machine license that can only be used in one lab (if you have 2 labs with half the number of computers you need to buy two licenses).
Also, we have to pay this price annually and we can't move the licenses from one lab to the other without a permission. Also, nothing done with this license can be sold. Is just for educational use.
Maya, Lightwave and XSI have similar offers. Not sure about Macromedia Flash.
For 3D, as mentioned before there are many cheap or even free alternatives.
2D though, Moho is probably one of the best tools you can get at the moment.
With 3D, Blender is great but has a large learning curve due to it's efficient but non-explanatory interface. http://www.blender.org
As long as the class is project orientated and more than just 2 weeks, it's well worth your time.
Yes, I did some research and the only other option would be for Flash because of the possibility of teach in other class game creation for web, but for animation, I believe Moho is the best option.