MS OneNote
Prawn, I name my chapters too, and whether or not they're used in the final product doesn't matter--they help ME tremendously

As far as organizing goes, I use MS Office OneNote in lieu of a table of contents. I am a non-linear writer (and also a very,
very right-brained writer), so while I write an intensive plot spreadsheet in the beginning, I tend to write the scenes as they come to me--which is never in the order in which they occur

My WIPs were a MESS before I got OneNote, and now I'm actually getting more done because I don't have to mull over the placement of a scene because it's a lot easier to move things. I also don't have to waste time "looking" for something, or trying to move things around in one big Word document. When I need to make a change, all I have to do is click and drag anymore. Something else that's great about OneNote is that I can also create sections and tabs for outlining, characterization, setting, and whatever else I think of. It's wonderful!
When you're ready to put your novel in Word, you can use the command to export your notebook to Word, format it in Word for submission, and voila! You're done
This may not be what you meant as far as organization, but I definitely wanted to throw that out there for anyone who is looking for that type of thing while reading this post. It comes with MS Office 2007 Home & Student Edition, or you can get it as a stand alone program. I use it for taking notes in my university studies, as well as things I do with my family. If you have a SmartPhone you can install OneNote Mobile at no extra charge, and you can type notes from your phone and then sync them to your notebook next time you use your PC. It may not work for everybody, but as you can see

I'm very happy with it.