One thing I wish Github would do is allow for a more granular permission structure. It would be fantastic if we could allow people without github accounts do things like submit issues, or allow certain users (e.g. non-technical staff) only have access to the wiki and issue tracker.

Right now the permissions are centered around what you can do with repositories, it's very developer-centric. I think there is a lot that GitHub could do here to expand their service to be more applicable to an entire organization.