I stumbled across vroop.com while reading a little about daring fireball, which is the website for John Gruber (the creator of Markdown). Two people who care about the way software works in an intuitive, use-aesthetic sense. On Vroop I read mention of TiddlyWiki, a client-side “Personal Web Notebook” based on the whole Wiki shared document concept.
TiddlyWiki looks like it might be the non-linear thought processing application that I’ve been looking for. I often write stream of consciousness style, defining terms and grouping things as I go along. Usually this is a somewhat tedious task, requiring many passes to refine the core ideas. But the organic and self-organizing properties of Wiki, with the ability to automatically define entities by mashing WordsTogetherLikeThis, could provide me a way of writing and organizing on-the-fly.