Well, I'm quite happy using Sprint.ly (https://sprint.ly) to build our product. I think what makes it a good choice for software development are the things it does not have, like custom statuses, custom item types, time tracking. Also, it has sane defaults.

Their story format (As a ... I want ... so that ....) can be weird at first if you are not used to it, but it really helps focusing on the real benefits of a feature and segmenting your customers.