I recently wrote The Geek Atlas (http://oreilly.com/catalog/9780596523206/). The main tool I used was XMLMind XML Editor since the book was marked up using DocBook XML. Before I started doing the XML work I was writing using emacs.
Once the writing was done I submitted it to the publisher via SVN (each book had its own project) and then the book was converted to a PDF. I then used Adobe Acrobat Reader to mark up changes based on the proofread and copyedit. The book was actually put together in Adobe InDesign but I had nothing to do with that.