I try to get the best of both worlds. I keep notes in lots of separate text files. When I need to look at them as one big file, I use blosxom to string them together as html.

Let me go through that in a bit more detail. Blosxom is intended to turn text files into blogs. It slurps in a directory structure full of text files, and splurts it out in html, with all the standard blog navigation and view options. In other words, you can view your files by directory, by date, individually, or as one long file.

I use a blosxom plugin for Markdown, which lets me add readable formatting that gets converted into HTML.

The text editor I use is emacs. But I don’t think it matters much, as long as your editor saves files in text format, lets you flip easily between several dozen files, and doesn’t take up much screen space (you need room for a browser to view your stuff).

I use this system for most of my notes - academic course work, other projects, things to think about. My todo lists would be there, but I keep them on paper instead. Over the year I’ve been using the system, I’ve written about 200,000 words of notes, and it’s all easy to access.

The big advantage over a text file is that it can cope with you doing fairly large projects inside it, without getting in the way of everything else. Most of the preparatory work for my dissertation happened in emacs/blosxom, for example.

There’s an added bonus in that it’s all accessible over the web, which is good if you’re using lots of computers. I even kept a public version (now semi-defunct) for a while, with the personal stuff removed by shell scripts.