I think the integration with JIRA (which is arguably best-in-breed for moderately heavy-duty issue tracking) is quite a compelling argument for going with an all-Atlassian setup; you can even use their SourceTree product as a git GUI.
On the other hand, GitHub's stuff generally does feel nicer to use and better and more thoughtfully UX'd.
Side note, but you can use SourceTree regardless, right?
I assume it has some features that are paid (or only work with Bitbucket?), but I've found it brilliant for managing GH repos - one of the nicest free tools I use.
Nope, SourceTree is now 100% gratis. You still have to "register" it and apply a key after 30 days, but this involves a simple signup form on a website.
On the other hand, GitHub's stuff generally does feel nicer to use and better and more thoughtfully UX'd.