I write mostly in Markdown using VIM or IAWriter with a scattering of LaTeX for some complex formatting. I have some Rake-based automation that hooks into pandoc to take the content and generate PDF, ePub, Mobi, HTML etc formats. You can see an example of the finished product in the sample chapter from one of my other books: http://www.logstashbook.com/TheLogStashBook_sample.pdf.