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I am currently formatting a manuscript into ebook formats (epub and mobi). My manuscript contains many footnotes, and I don't know how to handle them.
It's important for me that these be footnotes rather than, say, endnotes - they're humorous asides; I need the user to be able to glance at them and be able to get right back to the main text (and also, not to get a peek ahead at the next dozen footnotes from future chapters...).
I'm interested in both officially supported markup for major devices (I know the Kindle Paperwhite now has inline footnote functionality), and in workarounds which produce a good final result.
Kindle footnotes:
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If you're producing PDFs, their physical layout will be honored to a degree, then you can just use a PDF production tool which understands footnotes.
PrinceXML has high quality footnote support, as well as a styling language you already know (radically modern CSS3,) as well as basically everything else you would ever dare to want, as well as a startlingly active forum where users give compellingly weird solutions to really complex problems. However, it's rather expensive - five hundred, last I looked. (I love it, so I bought it.)
There is a free similar tool called WEasyPrint, but since I had Prince before WEasyPrint existed, I haven't had any reason to switch, and as such I cannot speak to its quality. I hear good things.
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If you only are afraid of your users reading the other footnotes if they are displayed as endnoted, then it might suffice to put each of them on their own page.
If you include an explicit back-link to the original location for the footnote at the end of the footnote ([continue reading ...]) as well, the reader is more likely to get back to the position they came from to read the foot-/end-note.
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I don't think there is an official way to put footnotes, at least in EPUB2. What I do in the ebooks I prepare is to add an hyperlink to the note (placed in a chapter of its own at the end of the book, and to put at the end of the note another hyperlink which goes back to the original position. It's a bit ugly, but at least it helps readers (in the sense of people, not devices!)
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There's no easy and global solution to it. I'd recommend using some kind of side-notes as described here.
Note that if your target is mainly EPUB3, you can create popfootnotes as described here.
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