TiddlyWiki is very flexible, and there are many different ways to use it. Here we're focusing on using it as a standalone file in the browser, which is a good choice for most users as it doesn't require any special knowledge or tools. For more options you can also run TiddlyWiki on Node.js. Video Tutorials are available, too.

TiddlyWiki - a reusable non-linear personal web notebook

TiddlyWiki - a reusable non-linear personal web notebook
Scrivener “The biggest software advance for writers since the word processor.” —Michael Marshall Smith Grow your ideas in style Scrivener is a powerful content-generation tool for writers that allows you to concentrate on composing and structuring long and difficult documents. While it gives you complete control of the formatting, its focus is on helping you get to the end of that awkward first draft.

Scrivener

MultiMarkdown - fletcherpenney.net “As the world goes multi-platform with all of the new mobile operating systems, MultiMarkdown provides an easy way to share formatting between all of my devices. It’s easy to learn (even for us mortals) and immediately useful.” — David Sparks, MacSparky.com “Personally, it’s changed my game — it’s how I think now. Can’t imagine writing more than a paragraph in anything that doesn’t do MMD.” — Merlin Mann, kung fu grippe MultiMarkdown - fletcherpenney.net