I'm planning to build a stack for internal company domain knowledge, and I've been thinking about middleman (http://middlemanapp.com) instead of Jekyll.

Middleman has impressive workflows and markdown processing (I'm guessing parallel to that of the Github/Jekyll solution or better). Also conrefs can be implemented by simple partials (which makes less contention for the probably huge conref file)

Though I have to be convinced by trying the Github/Jekyll stack, this does open my mind regarding Jekyll 2.0. I'm happy to see Github tell us their Jekyll story :)