I just discovered that Apple's Pages can export documents into .epub (in that sense it's a similar suggestion to Scrivener, which I'll have to try out next). I've tested the Pages epub export feature with text documents that included images, tables and footnotes - all were converted into epub without issues (i.e. I confirmed that it looked and worked as expected on an iPhone, with the Adobe Digital Editions app and that the files could be opened with Calbre and Sigil).
[Update] I see that there is an excellent discussion of the pros and cons of exporting epub from Pages and Scrivener on the ThreePress Blog.
On a related note, if you're specifically targeting the iphone/ipad I know that there was a session at WWDC 2011 that described best practices for how to create both flowing text and fixed layout (epub based) ebooks (including features like embedded HTML5 video and audio) for these devices. Unfortunately the content of the video & the slides for the session are still under non-disclosure. Check back in a few weeks if you're not a registered Apple developer.
