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Nifty - Manage projects, work, and communications in one place.
GitHub Visualizer - Enter user/repo and see the project visually
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.
CodeFlower - CodeFlower visualizes source code repositories using an interactive tree.
Asana - Asana project management is an effort to re-imagine how we work together, through modern productivity software. Fast and versatile, Asana helps individuals and groups get more done.
Gource - Gource is a software version control visualization tool.