My idea of having a module to generate a Maven site with the markdown syntax raised some interest — I received a couple of emails since then.
Tonight, I have made a quick and dirty Doxia module based on the MarkdownJ library.
I’ll try to publish it tomorrow. At least, I should bring the doxia-module-markdown project page back.
Edit: I don’t maintain this project any more. The good news is that there is a fork on github.