Unsolicited product endorsement: I'm a big fan of Scrivener, a Microsoft Word alternative that focuses on writing instead of thinking about how one's writing is going to look. The basic idea is that writing long works is more efficient if they're split up into manageable pieces. Scrivener helps me do this and helps me keep them organized. It's been a great tool for working on my book project (Are Species Real?) and even sketching out some new stuff for my second book (The Nature of Biological Classification). My basic workflow is to write/organize using Scrivener, export to word, and then use EndNote X3 within Word to format my bibliography. Fortunately, I can still drag references into my Scrivener file and my interaction with Word amounts to selecting a menu item ("Format Bibliography") — though I've still had Word crash hard at that moment! I've heard that the new version of Word for Mac is better, but of course it breaks EndNote integration until v.37 of EndNote is released (or whatever we're up to now).
I'd really encourage anyone who detests Word to give this workflow a shot. A trial version of Scrivener 2.0 was just released in connection with NaNoWriMo which will give you quite a bit of time playing around with the program. I haven't used the new version much, but so far it looks like a pretty significant improvement over the already great v.1.5.