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,
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. =)