I am trying to use wp-markdown and SyntaxHighlighter Evolved. SyntaxHighligher uses shortcodes (or pre tags with a special class). I've tried to get the shortcodes to work, however wp-markdown messes with them on the conversion causing funky results. This really just boils down to shortcode support. In one of the issues you mentioned wanting to support them; is this still on the horizon? Perhaps there is a workaround?