My first reaction to your question was to say, "Whatever system you choose for tracking homework, you need to make sure you review your system frequently and regularly." Learning happens best when you take your time to do your work; cramming a task into the last hours before a due date doesn't do you as much good.

If I were taking classes again, this is how I would use GTD to organize work for those classes. Each course would be a project; class meetings would go on my calendar (hard landscape, nonnegotiable), and assignment due dates (and times) would, too. Part of my regular (daily?) review would include looking ahead one to three weeks for due dates (the bigger the assignment, the farther ahead I'd look for it). Big assignments would be sub-projects with an associated list of next actions. My contexts would not be tied to homework, but to types of activities (e.g., reading, journaling, writing/drafting/brainstorming, talking, thinking, working problems, coding).

You should also consider the classic 43 Folders machine (a.k.a., tickler file) as an ideal tool for organizing class-related work.

But no system, with any numbers of bells and whistles, will replace vigilance and consistent review of what needs to get done and when.