If you plan on needing much in the way of cross-references (i.e. like in documentation where you're linking to other things all the time), you can use a slightly more advanced markup language like rST (reStructuredText) which is used by Sphinx (though it also supports Markdown). Sphinx docs can be output to a variety of formats, including epub, single-file HTML, PDF via LaTeX, and of course, a multi-page HTML site.
Comments
If you plan on needing much in the way of cross-references (i.e. like in documentation where you're linking to other things all the time), you can use a slightly more advanced markup language like rST (reStructuredText) which is used by Sphinx (though it also supports Markdown). Sphinx docs can be output to a variety of formats, including epub, single-file HTML, PDF via LaTeX, and of course, a multi-page HTML site.
And AsciiDoc seems roughly equivalent to rST.