I saw a reference to a "zettelkasten", a system for hierarchically organizing index cards containing knowledge, about 6 months ago. Interested by the idea, I put together some code to automate the process to some extent and started using it. It stores notes in a directory tree and provides commands to make it rather quick to move through the tree and print/edit things. Personally, I've gotten good use out of it: it provides some basic structure to my notes, and by aliasing the command name to something really short like 'zk' it's pretty quick to use, so I'm getting a lot better about taking notes.

Unfortunately, I wrote this in odd free moments at work and can't just release it without going through a rather convoluted process. It's only about 400 lines of Go, though, so anyone who thinks this sounds kinda neat should be able to replicate it pretty easily.

Oh, it also has commands that let you store a copy of a given file with the current note, so you could e.g. take screenshots as you're making notes and they'll live with the note.

Edit: I've played with org-mode but it's kind of a big beast and I like separating out all my notes into individual files, plus I'm only occasionally an emacs user (I get the bug, use it for a week, then get sick of it and bail out)