I've used Scrivener on Windows and Mac for a few years now, and I can say that it is worth the learning curve, especially with a large and gnarly project. But don't let the "learning curve" part worry you--just use what you can comfortably use and the rest will follow. That's how I started. Now it's much more natural to fluidly add meta-tags, keywords, document notes, annotations, internal and external links, and so forth and so on. Basically, it's an industrial strength piece of writing software for professionals or prolific amateurs, and the price is excellent. There is a significant downside, however: I find the iOS version is very bad. If working on an iOS device is important to you, be absolutely sure you check that out.
