I use tiddlywiki to implement any organisational model I want. My day to day work and knowledge base is managed inside a tiddlywiki and evolves with me.
From many of the tools mentioned here I can extract the algorithmic approach and incorporate it in my tiddlywiki, or package it for use in any future tiddlywiki. People with javascript coding should avoid reverting to it before they learn the wikitext and macros within tiddlywiki.
Personally I believe tiddlywiki is also an ideal platform on which to publish open source projects because it can be a document, an editor, a demo, a software dev kit and more (all in a single html file).