If you haven't seen it, I highly recommend checking out TiddlyWiki. It's an entire wiki that is stored in a single html file. I'm really impressed with what people are doing these days with JavaScript.
Anyway, I've been using TiddlyWiki to keep track of todo lists and a bunch of miscellaneous notes. I keep the html file stored in a subversion repository so I have a history of changes, and so I can easily keep my local copy of the wiki up to date on different computers.
Also, this plugin combines TiddlyWiki with jsMath, so you can use LaTeX to format math in your wiki.
