Scrivener
Writing a book, short story or research paper is about more than hammering away at the keys until it's done. Research, scrawling fragmentary ideas that don't seem to fit anywhere yet, collecting faded photos from old newspapers, shuffling index cards to find that elusive structure - most writing software is only fired up after much of the hard work is already done. Enter Scrivener: writing software that stays with you from that first, unformed idea all the way through to the first - or even final - draft. Outline and structure your ideas. Take notes. Storyboard your masterpiece using a powerful virtual corkboard. View research while you write. Track themes using keywords. Dynamically combine multiple scenes into a single text just to see how they fit. Scrivener has already been enthusiastically adopted by best-selling novelists, academics, lawyers, script writers and journalists - whatever you write, grow your ideas in style.
Nice companion for MultiMarkdown.