The RPG Dumping Ground has a great little introduction to Tiddly Wikis. I link to it because I used a GTD Tiddly Wiki to organize my own campaign material for several years. For me, it was the perfect way to drill down into the nitty gritty of world creation. I'd just start writing about some aspect of a world or campaign or character and then flag new terms for future development simply by making them into WikiWords. Then I could pick an undefined WikiWord and repeat the process indefinitely. Of course, having lots of time on my hands in those pre-parenthood days led to some rather large and unwieldy Tiddly Wiki files. But it was an amazing tool that is still paying dividends as I look back to mine my old campaigns for new material.
These days, however, I've moved most of my world-building to the Cloud via Google Sites. I get similar (though not quite as seamless) wiki capability with less sensitivity to size and more freedom to format things as I please. Additionally, I can open up world-building to others by granting access to collaborators.