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 Project Management - No-fluff guide to building a collaborative development team
Create Issue Branch - Automates the creation of issue branches on GitHub
FoldersLint - Directory structure linter for JavaScript projects
REVISR - Git Management for WordPress : keep track w/ version control
GitScrum - Project management tool for agile teams.