One of the reasons that footnotes have had a bad time on the Internet is that they are a peculiar macro-typographical feature that HTML lacks a capability to handle. What browsers are good at is fetching in all sorts of foreign bodies and bringing them near to hand: so-called replaced items, such as graphics, can be fetched (if you so wish) from a server in Europe, combined with a text page from a server in Asia and integrated on a computer near you. Frames and of course hyperlinks play similar tricks.
The footnote, which is part of the text, has to be pushed away for display, when needed, in a remote location, at the edge of, or off, the screen. In a sense, that is the antithesis of what hypertext is all about.
It hardly makes us love visual browsers when we see how well the word-processing program WordPerfect for almost a decade has handled the creation of footnotes on paper output: on screen during the writing phase, you can edit the notes right where they appear using the "Reveal Codes" window, but in print they are all tucked neatly at the bottom of the printed sheet. MS Word has almost caught up, without being quite as user friendly.
However: convert an MS Word document into a HTML page and you'll see the full horror of the messed-up footnote. Out of the box, MS Word turns them into endnotes, using full-size numbers in square brackets for both links and return links. Not only do they look ugly, but they are tiresome to read.
Everybody is aware that visual browsers make a pig's ear of displaying footnotes, but the answer is still taking shape. In 1998, the World Wide Web Consortium (W3C) noted the lack of provision for footnotes in the Cascading Style Sheet system. One likely solution in the next CSS standard, CSS3, will be better provision for pop-ups, fired by hover, as one display method.
It would be useful too if spans of text declared as footnotes could be reflowed below larger divisions of text (paragraphs, printed pages, or chapters, for example). However the current draft of the CSS3 Box Model does not provide for this.