For the GTD stuff, I use emacs + org-mode + .emacs based on this configuration + mobile org.

Since I try to work exclusively in emacs, I can quickly capture notes and "things that need to get done" in their proper context, all of which is aggregated under an Agenda window. The Agenda window manages a collection of ".org" files which store the specific details of everything. MobileOrg syncs all these .org files to my phone. Combined with the GTD philosophy of never having anything uncategorized bouncing around in my mind, this system works very well for me.

Example workflow (a better and more complete example is in the configuration I linked above):

1. At the end of class, Professor assigns a programming project due in a week. I pull out my phone and quickly capture a TODO item with a deadline in Mobileorg. Mobileorg syncs this to google calendar.
2. I get home and pull up the agenda in emacs. The item referencing the programming project shows up in my "Tasks to refile" category (equivalent to "Inbox" in GTD terms), along with any other TODOs I captured while I was at school.
3. I refile the project to an org file that contains all the information about my classes and define a NEXT item under it, which represent the next action I need to take on the project. When I start working on the project, I can attach any files related to it directly on the TODO item identifying the project.
4. The NEXT item shows up on a list of NEXT items on the agenda. I can filter these by project (defined in the GTD way) or by the tag system.

It all seems very complicated, but all of this is literally a couple of keystrokes. And this barely scratches the surface (take a look at the aforementioned configuration to see what I mean).

Pros:

• Forces you to learn emacs.
• Easily configurable and incredibly robust.
• Optimized for functionality rather than prettiness (i.e if you end up liking it, you'll know it wasn't because of the nice UI, which is usually the main selling point for any computer based organizational system).

Cons:

• Forces you to learn emacs.
• Takes a huge amount of effort to set up. I would compare it to setting up an Arch Linux system.
• Can get messy if you don't know what you're doing.
• Getting the syncing functionality isn't easy.

A spaced repetition package is also available for org-mode, which really ties the whole thing together for me.

EDIT: You can also overlay latex fragments directly in org-mode, which is really nice for notetaking. Whole .org files can be exported to latex as well.