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.
GitHub Visualizer - Enter user/repo and see the project visually
Nifty - Manage projects, work, and communications in one place.
CodeFlower - CodeFlower visualizes source code repositories using an interactive tree.
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.
SyntaxDB - Easily look up programming syntax for multiple languages