Scrivener, the dedicated word processor for fiction writers. This used to be a Mac-only affair, but a Windows version is now in beta, and anyway I've switched to a Mac laptop for my writing. (Sorry, Ubuntu, those were good years.)
My awareness of this app comes at a time when I have been quite vexed by the problem of re-organizing a book that contains dozens of small chapters, which I am doing now. In a conventional word processor (in my case, OpenOffice.org), this is a really annoying task. In Scrivener, you can assign each chapter a note card, on which you can type a summary of the chapter; then, on a "corkboard" screen, you can rearrange the cards at will. When you're finished, you can export the whole thing as a unified .doc or .odt.
I think it's too late for this novel, but I may switch over for the next. If any of you are Scrivenists, please share your thoughts.