I do all my thinking on paper, but I have a large blocker at the moment: indexing my notes. Have you found a good solution for this?
I don't think I'm doing a good job of explaining this, I'll see if I can find an example of this online and link it.
Edit: I did a quick google search and found an example that's similar to what I'm doing. This works well for me: http://lifehacker.com/mark-page-line-edges-to-organize-your-...
More ephemeral things like todo lists, I only scan if I have a reason to want to keept it.