The immediate solution to the problem is not to use footnotes. Footnotes are a pretty good indication that you are not writing something well. Either you are trying to say too much, in which case the footnotes are clutter; or you have not organized your prose effectively, forcing you to use hypertext; or you really want to use hypertext. In the latter case, make a link and write the page.
However, most of the time you do not have enough content to make a good page. Footnotes in this case are more like a prototype of a ShallowPage. But ShallowPages are often seeds of larger ideas. We would like to be able to refactor the footnote to its own page easily. We might also want to create annotations, a hypertext formation we have avoided so far with wikis. Annotations are great if you want to create a glossary of terms or you want some form of endnotes for a big ball of ideas.
Therefore, use NamedAnnotations that point to PermanentAnchors.
Blah blah [[^FooBar]] blah blah. ... [#FooBar] This is my footnote, endnote, whatever. (may be on a separate page, such as a glossary?)
The parser would render the footnote simply as <sup>*</sup>. This is simply a cue to render the reference of the PermanentAnchor in an inoccuous fashion (superscript *).
PermanentAnchors free you to rework with the organization of all the notes, possibly into new fuller pages without having to undergo the expensive of reworking all the references. They also are WhatYouSeeIsWhatYouGet? syntax.
At the ultimate cap on FeatureKarma, you may not even want to replace the footnote with a *, but instead just use a directly rendered citation to a PermanentAnchor, as we frequently do with pages. a la (cf. PermanentAnchor) This way, you do not need to add any more code to the script, but instead just use the PermanentAnchor system.
See also NamedAnchorsInWiki, CommunityWiki:FootNote.
See also AnnotationWiki if you are interested in third-party annotations to static web pages.