GitHub Enterprise is an on-premise product and separate from the "dot-com" (GitHub.com) product offering. Inside Microsoft we have great engineering systems that today are powered by Visual Studio Team Services (VSTS), so for most teams we try and use that for all private engineering work.

For our externally-facing open source projects, we are using the GitHub.com public product like any other GitHub user - we realize that GitHub is where open source lives these days!

That said, we have some unique challenges, as we have nearly 10,000 members in some of our organizations.

Full disclosure, I work within the Microsoft Open Source Programs Office and am responsible for our GitHub.com billing arrangements at this time.

These companies run their own internal git systems (Gerrit & Team Foundation Server). They put their OS stuff on GitHub, which only charge for private repos.