I had a similar experience in my undergraduate program (and I graduated over 8 years ago). In second year, everyone has to take a software engineering course that consists of completing a full waterfall model group project. It was complete with interviews with the clients, every scrap of planning documentation, and of course the code itself. Each deliverable was due every 2 weeks and everyone had to work their ass off.

Future courses covered agile methods, version control, bug tracking, database design, and so on.

I actually feel a bit sorry for people who end up going through a program like Joel describes -- but certainly good schools are out there and they're teaching things programmers really need for the real world.