While not strictly a Flask-dependent module, Coaster offers an implementation of GitHub-flavoured Markdown as a convenience feature.
GitHub Flavoured Markdown: because normal markdown has some vicious gotchas.
Further reading on the gotchas: http://blog.stackoverflow.com/2009/10/markdown-one-year-later/
This is a Python port of GitHub code, taken from https://gist.github.com/Wilfred/901706