We currently use FogBugz with GitHub (private repos) and it works very well. I wrote a bridge that connects both APIs together, so we get fairly good integration. Information about commits and branches gets attached to FogBugz cases and we get a smooth workflow out of it.
The problem with FogBugz is that it is slow and has a number of minor annoyances, which grow to be a pain in the long term. Such as Fog Creek refusing to make the software automatically mark "#1527" as a linkable case. You have to write "case #1527". Quite annoying, especially if you don't run your FogBugz installation in English!
There are other things, such as obsolete Windows-based character encodings they insist on using in E-mails sent from FogBugz. Also, hosted FogBugz is slow. We spend a lot of time waiting.
Oh, and the default "VCS integration" features in FogBugz are from the CVS/RCS era and they still haven't been modified, even though they sell Kiln. The "Checkins" field in every case is file-based, so there is no way you can attach modern DVCS changesets to it.
I reported all of the above problems more than a year ago, and nothing has changed.
All in all, while we do use FogBugz (and pay quite a bit of money every month for the pleasure), we are looking for alternatives.