For making notes I wrote an open-source hierarchical plain-text editor Notilo. It is basically a Notepad with tree structure. There were a few similar programs, but none of them had all of the features I wanted (free, Unicode, saving in database, no special syntax). The program is not finished yet; it works correctly, but it should be more pleasant to use and better optimized for very large documents. (I have stopped the development when the proverbial 20% of features fulfilled 80% of my needs.)
In real life I keep a bunch of A7 papers (for US readers: a letter size cut to 8 pieces) in a plastic envelope and a small pen. The papers are small enough to put in my pocket and bring almost everywhere. Later I write the notes to computer and discard the used papers.
Recently I made a habit to write down almost everything I learn about programming (that's my job), because I have noticed a knowledge loss when I work with some technology, then a few months or years I work with other technology, and then I come back again. This didn't happen to me when I was younger, because when I moved to a new technology, I did not return to the old one, but these days I am using a few different technologies in parallel.
(Once I thought that having a "personal wikipedia" could be great, but I don't want to put private information on internet and running a web server on a personal computer makes it very slow. But there are some programs that provide similar function without the web server.)
Today the computer media are cheap and it is easy to record anything. Problem is, your day has only 24 hours and the Moore's law ain't gonna help you about it. It could be interesting to record every conversation you ever had, but when will you listen to them? And what is the point if you won't? You need to system to search your database; at least provide some keywords to each conversation, so you can search the keywords.
Recently, I've collapsed (ascended?) down/up a meta-learning death spiral -- doing a lot less of reading actual informative content, than figuring out how to manage and acquire such content (as well as completely ignoring the antidote). In other words, I've been taking notes on taking notes. And now, I'm looking for your notes on notes for notes.
What kind of scientific knowledge, techniques, and resources do we have right now in the way of information management? How would one efficiently extract useful information possible out of a single pass of the source? The second pass?
The answers may depend on the media, and the media might not be readily apparent. Example: Edward Boyden, Assistant Professor at the MIT Media Lab, recommends recording in a notebook every conversation you ever have with other people. And how do you prepare yourself for the serendipity of a walk downtown? I know I'm more likely to regret not having a notebook on hand than spending the time to bring one along.
I'll conglomerate what I remember seeing on the N-Back Mailing List and in general: I sincerely apologize for my lack of citation.
Notes
(I've also heard a handful of individuals claim that SRS has helped them "internalize" certain behaviors, or maybe patterns of thought, like Non-Violent Comunication or Bayes Theorem... any takers on this?)