The habit of fighting confusion with pen and paper is for me one of the biggest productivity boosters I've ever learned.
Also, I don't like to do this kind of "brainstorming" on computer - hardware&software are too limiting, both in input and spatial presentation. Free-form noting FTW ;).
When I start to work on a task, I open up onenote and break that task in to sub tasks that are more bite sized (a la pomodoro) that I can strikethrough when I'm done. Strikethrough you can add to your quick bar in Office 2010. Using onenote I can expand subtasks if I find they're too large, and if I have to stop working on task A to go to B I know approximately where I left off. Inserting text is difficult on paper.
When all the subtasks are done I delete it from onenote and strike it through on the paper.
Pomodoro is a bit too rigid for me in the office where anyone in the cube farm can interrupt you any time of the day, but it certainly did help me crunch through my 10 page paper during my last semester in college.