One nice enhancement would be a simple toggle for hiding labels with no issues.
The lightbox approach to presenting an issue seemed a little funky - mostly in that it just feels like it is not a "real" part of the interface since it is shown in a small column. I also noticed some issues with URLs overflowing the lightbox.
Speaking of GitHub Issues - the biggest, simple change I can imagine GitHub making to Issues is allow repository owners to add a small readme to the New Issue page. It would help a lot in explaining what a good bug report looks like and where else to get help.
As for the lightbox part, there's indeed a bit more work in representing the content of the issues.
1. Adding issues: I want to see everything
2. Triaging: I only want to see labels with issues
Thus, most of the time I want only those with issues, or all of them.TaskTub: http://www.tasktub.com/authentication/login Waffle.io: https://waffle.io/ BugHub: http://bughubapp.com/ (though since abandoned?)
Sprintly also has awesome Github integration, but they are explicitly NOT a front-end for Github Issues, so works best with private repos for larger teams (imho). They integrate well with Github, not necessarily Github Issues (a slight, but key difference).