I’m always behind the times. I just discovered Tiddlywiki and I love it!
I’ve always wanted to start a series of notebooks like Cosma‘s and TiddlyWiki seems like the perfect fit. Indeed my discovery of TiddlyWiki was inspired by a similar notebook project by a famous surfing physicist. I’ve started up using a personal TiddlyWiki for keeping a working journal/projects/todo and so far I am really liking the functionality that one can get. There are an amazing amount of plugins written for TiddlyWiki (LaTeX functionality is pretty smooth), as well as TiddlySnip which is a Firefox plugin for directly importing from web pages (note that you need the newest version to work correctly with Firefox 3..see here.)