[kiba]

My only problem is that I have no way to do easy footnoting. I had to add my own special HTML code at the bottom of the page, manually verify the link, and so on. Too much work.

[masklinn]

There's always reStructuredText/sphinx as a bigger markdown, it has extensive support for linkage including footnotes: http://docutils.sourceforge.net/docs/user/rst/quickref.html#...

Without even delving into Sphinx's extensions.

[dfc]

Pandoc extension for footnotes in markdown:

Here is a footnote reference,[^1] and another.[^longnote]

[^1]: Here is the footnote.

[^longnote]: Here's one with multiple blocks.

[hiltmon]

FYI MultiMarkdown by Fletcher Penney adds footnotes to standard Markdown, see http://fletcherpenney.net/multimarkdown/