@roger64: Many apps, for example Calibre, use
heuristics to detect footnotes and display them in popup windows. I.e., you won't have to convert your ePub2 books to ePub3 books to get popup footnotes.
Some time ago I did some tests with different ePub3 footnote types and believe that rear-notes (end-notes) wrapped in aside tags, are best in terms of ePub2 and iBooks compatibility. (The last two footnotes in my test ePub are encoded in this way.)
Here's a short app compatibility breakdown:
iBooks: only footnotes 1, 4 and 5 work; they're rendered as popups
ADE: only footnotes 2, 3, 4 and 5 work in ADE 1.7-4.0
Azardi Reader: only footnote 1 is rendered as a popup footnote; the remaining footnotes are rendered as end-notes.
Gitden Reader/Namo PubtreeViewer/Calibre: all footnotes are being displayed as popup footnotes
For mobile devices I'd definitely recommend the free Gitden Reader/Namo PubtreeViewer iOS/Android apps.