I use Literature and Latte's Scrivener for all my complex, multi-node writing. Love it. Can't wait for the iOS version to come out (oh please oh please come out soon).
They just came out with a beta of a new app called Scapple, which is awesome for two reasons. First, it seems to be a midd-mapping app that is even less restrictive than a mind-map. And second, it makes me think of scrapple.