This tracker app [0] is designed to be pretty modular, and there's a service implementation that uses the GitHub API client [1]. In theory, you could modify it and expand it to cover your custom needs for issue tracking.
We would love your thoughts on ZenHub.io [1] - fully integrated issue tracking, +1, estimates, burndown charts, kanban boards, even a personal todo list - a lot of the features asked for here, right within the GitHub interface and presented a lot more cleanly than competing products.
Looks nice. How do I add additional organizations after the first one? Can I send an invite to other organization managers to make themselves available for ZenHub?
Each organization is treated separately, all you need to do is install the extension and visit a repo of the other org. From there you'll start a 2 week trial and you'll be able to invite your team members and managers :)
waffle.io does this, but having to run on top of GitHub means it can't really fix problems like voting. But it can offer better search and things like that