Right now we have some search and charting features that GitHub's web interface doesn't. We also hope to do a much better job with PRs (diff view especially).

Right now we have some search and charting features that GitHub's web interface doesn't. We also hope to do a much better job with PRs (diff view especially). The big win for us right now (and hopefully other teams) is the ability to view issues from multiple repositories all together. So if you have an organization wide "1.0" milestone, you can actually view all the issues in that milestone from all repos at once. You can also use custom queries to group things however you like across all your repos.