At path11 we use AgileZen for out project and company planning (we treat path11 as a project more).
AgileZen (pivotal tracker too) is a very nice tool for managing your projects. There are a lot of different and similar tools out there, some really great!
As a developer type though I am missing things in all the tools I have looked into so far. The one that I miss most is real github and cucumber integration.
So this idea would be a web based management tool that is integrated in your repo.
You checkout the repo, run
start_p11 and woosh your browser opens up the tool that let’s you manage your project (moving stories around, etc).
As a bonus you would have the same app deployed, say in heroku so that your customers could interact with it as well.