A previous employer was dead-set against using Github's public site and insisted on using Github Enterprise. They were simultaneously resource-stingy and thus we had to bend around in all sorts of uncomfortable ways to minimize the amount of employees we had with Github Enterprise logins to keep costs to the bare minimum. Needless to say, this was a messy and stupid situation.

Perhaps there are some companies for which Github Enterprise makes sense, but it seems like the number of potential matches for it being a really good fit is small. Most companies should just use Github.com or if they really need to keep the code out of "the cloud", just use plain old git with gitlab, gitorious or plain old ssh access control.