The best system is the one you grow yourself. How do you take notes?
I mindmap a lot. Although mindmapping on paper is a lot of fun, Freemind's keyword shortcuts lets me mindmap nearly as quickly.
I haven't opened Freemind in a while, though. Can't be bothered to switch out of Emacs. My talks usually start out as text outlines. I don't write it all in one swoop. I type random keywords, backtrack, fill in, rewrite... Sometimes I pull out a sheet of paper and redo my mindmap there, reorganizing it in the process. When I'm happy with the sequence, it gets turned into OpenOffice.org slides.
For random snippets, I use Planner because it's so easy to blog text from my current window. People who use web browsers a lot might want to check out Bloglines, del.icio.us, QuickNote, and other Web annotation tools.
I think that making it easier to get stuff out of your head is the first thing you have to do. You can worry about the quality of said stuff later. ;)
As for the note about extreme programming: you might want to check out David Allen's Getting Things Done method. It emphasizes focusing small accomplishments and reflecting. =)