I love this plugin. Works great for the comments on my site.
I've recently started using bbPress though, and have enabled WP-Markdown for forums/topics/replies. What I get when saving is pretty weird. There are literally
<p> tags being saved, and then those literally display when the reply is posted. Editing the post gets you pretty weird stuff as well, which alters the content when re-saved. Ideally, what a user writes is displayed again exactly how they originally wrote it, and the weird P tag thing doesn't happen.
Here's a little screencast showing the issues: http://www.screenr.com/EtCH