A good place to start learning about David Allen's famous method is to read his book, Getting Things Done, but even without that, there's plenty of information available online from Allen and others about the techniques and tools you can use to follow the GTD lifestyle.
GTD Times, the official blog of the David Allen Company
The Urgent & Important Matrix, also sometimes called the Eisenhower Matrix or Covey Matrix, is a method by which you can prioritize the things you have to do to take care of the most high-impact tasks first. The Joint Information Systems Committee has a short guide to the system that it includes as part of a larger InfoKit on time management techniques.
If you struggle with finding a to-do list that works for you, perhaps you should look at the problem from a different angle. Eric Barker wrote a piece in The Week in which he talks about Georgetown University professor Cal Newport's plan -- rather than creating a list of things to do for the day, he schedules everything he does. It's simple and effective, and it might work for you, too!
Dr. Newport also has a blog called Study Hacks, which may also be of some use to you as you seek greater academic productivity.
Asana is really designed for groups to get work done, and it's easy to assign tasks to others if you'd like to use it to create group projects, but you can also use it for personal to-do lists. Not only can you add subtasks, but you can also group tasks by discipline.
If you'd like a little help prioritizing your to-do list, consider Toodledo, a task manager that analyzes your entries based on date, priority, and task status. You can sign up for a free account and use it over the Web or via iOS, Android, and BlackBerry clients.
Trello was created by Joel Spolsky (formally of Microsoft) and Michael Pryor, founders of Fog Creek Software. It's a free tool to help you manage collaborative projects. It's easy to use, and offers a simple drag-and-drop interface.
WorkFlowy is a very simple, easy-to-manage to-do list or outliner. You can customize its look and it works well in mobile browsers, too. While its simplicity and lack of flash may put some off, others prefer its down-to-earth functionality.
Wired's GeekMom: WorkFlowy is the Best ToDo List Browser App