If you do your writing on a Mac, and haven't already heard of Scrivener, you may want to check it out.
I'd been doing my writing on MS Word, with index cards in Mindola SuperNotecard, and logs and research in Circus Ponies Notebook, until someone pointed me at Scrivener. After an extended trial period (one of my favourite features), I finally bought Scrivener today.
It breaks out chapters really easily. It allows you to move them around. I can keep all my research in Scrivener. It remembers, in each chapter file I visit, my location in the file the last time I visited. Which makes flipping between scenes incredibly easy, without having to pepper the document with bookmarks. I can do outlining in a similar way to how I do it in SuperNotecard, but all within Scrivener. Synopses of scenes go on the "cards" associate with each scene.
The littlest thing that really impressed me? Scrivener has one of the sanest "try before you buy" policies for those who don't write every day. You get a 30 day free trial. But that's not "30 days from when you download". It's 30 days of actual use. So if I was at 27 days left on Monday, but didn't get to write again until Friday, I still had 26 days left of trial on Friday. Now THAT's considerate.
I think there's still room for Notebook in my writing life, but Scrivener packs a powerful, simple feature set into an affordable package - $39.95 USD. Windows users, unfortunately you're out of luck.