Recently I've been using Evernote to organize my notes. It has a nice phone app that I can use to take quick notes while away from my computer, a computer program, and a browser plugin that lets me clip articles. When it comes to notes I try to think that every time I record an idea I would have forgotten, it is roughly equivalent to thinking of one new idea.

I tend to write out outlines after I finish books or some interesting articles partially to see the arguments more clearly and to refer back to in the future.

It's always interesting/fun to go back browse old ideas I've forgotten about.