I teach various kinds of classes and have about 100 students per semester in total. I do a lot of my organizational management via gMail, by automatically labeling emails that come in from students, organizing them into their separate groups, and automatically sending back instant responses.
gMail actually makes doing all this very easy, but it is a multi-stop process. To simplify things, I have put together this screencast taking it step-by-step. Please let me know if you have any questions!