I had a post a while back about the use of Markdown which then got converted in to ePUB and then to MOBI for Kindle.
I've moved on from that to reStructuredText with Sphinx extensions.
It's a simple plain-text markup -- but far more flexible than Markdown.
It also has direct ePUB output support. The initial "epub theme" isn't super awesome for novels -- it is considered "experimental" -- and the entire tool was designed for technical documentation, but tweaking the theme is straight-forward. I'll be providing a link to the theme I use.
I use a script to give myself a little more flexibility. On its own, Sphinx is great, but I wanted some specific features that weren't available out of the box.
I'll be talking about this more in later posts. I think I have a system in place that will allow me to keep my world notes for all novels in a shared world together, plus single-source an annotated behind-the-scenes version of the novel along with the released version. I should even be able to manage the issue of edits and tracking changes/comments on the source without using Microsoft Word's "track changes" feature.