Ywriter (
http://www.spacejock.com/yWriter4.html) is a free word-processing program designed with the needs of authors in mind. It lets you easily break your novel down into chapters and scenes, and has tools for you to keep track of the status of your subplots and characters in each scene. Ywriter also allows you to easily move scenes around after they've been written.
I'm currently using Ywriter to edit my 2006 Nano novel; I'm not sure if I'm goingg to be using it for my novel this year (because I'll be primarily writing on my palm again), but it looks like it's generally speaking a pretty powerful tool.