Here's what I do1 to simulate footnotes:
These lines are _going to_ intersect<sup>1</sup>!
1. See Euclid's 5<sup>th</sup> postulate.
It's not that hard to do, but it's still a pain and the results aren't ideal. There's no easy way to set up links from the footnote mark to the footnote text and back again. Also, the footnote text ought to be smaller than then text in the body, but adding
<sub>...</sub> tends to break the numbered items and I don't bother to play with it usually. It also gets tricky when editing in a new footnote since you need to manually adjust the numbering of notes that come after. Compared to using advanced links, roll-your-own footnotes seems practically barbaric.2
PHP Markdown Extra has a really cool footnote syntax3 that I'd like to have available on Stack Exchange:
These lines are _going to_ intersect[^1]!
[^1]: See Euclid's 5<sup>th</sup> postulate.
Just writing that example makes me yearn for footnote support; even the Markdown code looks clean! The output is more professional looking than my manual footnote technique and includes all sorts of niceties like auto-numbering and inline footnote text.
1. All the time!
2. So why not just use links or parentheticals instead of footnotes? Because we aspire to the sort of answers expected in academia where footnotes are de rigueur. Plus it looks like you know what you are talking about and therefore encourages upvoting.
3. Suggested in the comments by Arjan.
<small>, @Shog9... ;-)