To foot note or to rewrite.
Don't footnotes make it really difficult to edit the source? Not really, if the syntax makes sense. In an email, they would be written as follows:
This is some text.  And more text. Footnotes:  This is the note.
This is tricky to translate into decent markup.
Another way is to inline them as some sort of super-parenthetical remark. Instead of using brackets (like this), use some more elaborate ((like this)).
On this wiki, we use double braces for footnotes. 1 The number links to the note, and the note links back to number, so you can read the footnote by following the link, and you can quickly jump back to where you came from. In addition to that, a small popup will show you the beginning of the footnote, if your mouse hovers above the number.
Using footnotes is bad style. If you want to write a footnote, maybe you are trying to say too much at once, or the writing is begging for better organization, or you are secretly thinking of making a new page except you don't know it yet. Some publications are full of footnotes, sometimes taking up to a third of a page. Some dissertations seem to be prone to this problem, the reasoning being that you want to provide extra support for the curious without breaking the flow of the text. For the curious, however, the flow of the text is severely broken. Putting footnotes at the bottom of the page is bad, but putting them at the end of a section is even worse. To rephrase the question: Do you really want to write text for the not-so-curious?
Don't confuse footnotes with plain references. References are bibliographical information. The referenced material is part of the natural flow of the text. There are tons of pages explaining how to do it. Google:citation.
Footnotes are a useful literary technique when you absolutely have to provide more context than the rhetoric of your argument allows. So are hyperlinks. On a wiki, footnotes are often be just ShallowPages in disguise. If you want to use footnotes for parenthetical remarks, why not use parentheses instead?
Often I write a statement which is not technically true, but which is much simpler and more concise than the technical truth, one which most people will understand because of context. Being the particular kind of guy that I am, I usually feel the need to put some sort of very long qualification in parentheses right afterwards. I would prefer to put this in a footnote so as to make the main body of text easier to read.
Many academics don't seem to share my stylistic goals. If there is something that is technically incorrect, but is a concise common-sense simplification, they just won't write it in an academic paper. Academic papers are expected to take a long time to read, because they cover a lot of details that a casual reader might not be interested in. In contrast, usually my goal is to save time for the reader.
I think of footnotes as a kind of SimpleView. They allow the same text to be read quickly, or for someone interested to choose to get the "full story" by reading some of the footnotes. They are, in fact, better than SimpleView because they are more like ZoomableViews; the reader gets to choose on a point-to-point basis if they'd like to spend their time to get more detail.
Well, this comment was pretty theoretical, so it won't really convince you that footnotes may make things easier to read, instead of harder. You'll see what I mean (or maybe I'll see what you mean!) as I use them.
Blah blah [[^foo]] blah blah. ... [#foo] This is my footnote, endnote, whatever. (may be on a separate page, such as a glossary?)
The parser could render [[^foo]] as a <sup>footnoteCounter</sup> if it appears on the same page. If instead it is a PermanentAnchor, it may be as simple as <sup>*</sup>. The advantage of a PermanentAnchor is that you can refactor the text elsewhere. This could be a nice inbetween solution for ShallowPages. I'm going to call this NamedAnnotations and write it up on MeatballWiki. – SunirShah
When it appears on the same page: Yes, it would work, but that requires more editing effort than the current solution. I like the current solution better.