Free Online Ebook Converter
It provides you with the best PDF to ePub converting experience.
We use http://sphinx-doc.org/ and author in ReStructuredText with some extensions. From that, we output HTML, PDF and ePub.
There are some issues with the ePub (they display fine, but don't validate), so it looks like sometime soon, I'll be hacking on Sphinx to fix some of the bugs in the epub generation.
I couldn't really be happier with this system.