Can anyone help me? I write lots of notes when researching articles and my university work. Right now I'm filling pages and pages of A4 with scribbles as I start my MA dissertation work, which I then type up. But they're quite a pain to organise, and even more so to find relevant notes later on. I keep notes in files for each book/paper/web page I take them from (e.g. notes-hacker-manifesto.txt). But then there might be a paragraph in there about a free culture ethic needing to reach beyond copyright to deal with, for example, education or people's actual ability to use software (as opposed to their liberal "freedom" to use it).

When I then come to write a section on "going beyond copyright" I'll want to find this paragraph, but I won't remember the files that contain relevant sections. Digging is quite boring! More organised people in ye olden days would colour code their pages. I'd like to be able to collect my notes by book/paper/web page, but then tag sections so I can quickly pull out notes by theme later on. I definitely want to group by the task at hand (e.g. MA dissertation, article for LWN on KDE4) but it would also be cool to be able to find all notes I've ever taken on a particular theme.

Is this possible? Has some benevolent hacker created such a program? I've looked at simple notes solutions like Tomboy or tagging web pages but they don't really fit the bill. Putting each paragraph into separate pages/notes would be really laborious. I just want to select a section of text and tag it. Or maybe somebody has a simple tip for organising my notes better without a snazzy tool?

edit: BasKet is no good either, I've left a comment explaining why. Do keep your suggestions coming though, there are some wacky methods!