See: github-flavored-markdown

As an npm package:

npm install ghm

And then in your node program:

var ghm = require("ghm")
ghm.parse("I **love** GHM.\n\n#2", "isaacs/npm")
// returns:
// '<p>I <strong>love</strong> GHM.  '+
// '<a href=\'http://github.com/isaacs/npm/issues/#issue/2\'>#2</a></p>'

To get the sha/issue/fork links, pass in a second argument specifying the current project that things should be relative to.