Hacker News Reader

I start out in Scrivener and end up in HTML. Scrivener is great for the actual writing process, although it takes a bit of learning to get used to.

I wrote up on my blog about creating the various versions http://rachelandrew.co.uk/archives/2014/01/07/html-epub-mobi...

I've also recently presented on how to build books in CSS and HTML and the slides and various useful resources are here: http://rachelandrew.co.uk/presentations/css-books

I highly recommend a LaTeX typesetting pipeline for producing the print version your book.

The fonts and page layout make for high quality books.

Using pandoc you can convert pretty much any modern markup language to .tex (I don't recommend .tex as the source format, as it might be difficult to get used to if you don't have experience with it + it is not trivial to produce .html/.epub from .tex sources.

I believe Tim Ferriss said he wrote his first book entirely in Evernote but now raves (with others) about Scrivener.

Keep up the good work.

Scrivener is what all the pros rave about. But if you wan't to check out another option, keep an eye on my sideproject http://blankpage.io :)