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Trello - Infinitely flexible. Incredibly easy to use. Great mobile apps. It's free. Trello keeps track of everything, from the big picture to the minute details.
Zube - Project management for developers.
Nifty - Manage projects, work, and communications in one place.
Huboard - HuBoard is built from the ground up using the GitHub public API.
Jira - The #1 software development tool used by agile teams. Jira Software is built for every member of your software team to plan, track, and release great software.
Codetree - You can manage your entire development process through GitHub.