Michael Froomkin sens us to:
Joho the Blog » Footnoter: I frequently write in HTML, but find footnotes (endnotes, actually) a pain. I don’t like having to interrupt my flow to jump to the end of the document to plunk in a footnote, and I hate having to decide on a number not knowing if I might decide to insert a footnote ahead of the one I just inserted. So, primarily because I enjoy writing utilities for myself, I spent far more hours writing a tool that will make it easier for me than the tool itself will save.
Footnoter lets you embed footnotes in the middle of an HTM document. [[For example, this might be a footnote]] It looks for the designated delimiters, pulls the footnote out, puts it at the end, and leaves a hyperlinked number in its stead. It defaults to the quick-and-dirty HTML that uses <sup> to superscript the number, but the Advanced section lets you instead insert CSS classes for the marker in the text, the marker that precedes the footnote, and for the footnote itself. Some warnings if you decide to try it out. First, It’s fragile. I’ve barely tested it. I’m sure there will be lots of ways it can be broken. (Nested footnotes won’t work.) Second, you would be a damned fool to paste its results over your only copy of the document you’ve been working on. Third, I am a baboonish, flatfooted writer of programs. What I write is the oppoosite of elegant: I prefer the long way of doing it and of writing it, since I can barely follow what I’m doing. Besides, the programs I write are so small and confined that efficiency doesn’t really matter.
If you care to try Footnoter out, with fear in your limbs and forgiveness in your heart, it’s here.