To use footnotes in markdown, use a <sup>-formatted link in the text and link it to the footnote at the bottom of the page, which should also contain a link back to the text that referenced the footnote.
An example:
This is the text that needs a footnote1
1 This is the footnote, which may or may not contain a link itself, but should end with a link back to the referencing text.⇧
See also: http://stackoverflow.com/questions/1696619/displaying-unicode-symbols-in-html