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.
Pivotal Tracker - Pivotal Tracker: The awesome, lightweight, agile project management tool for software teams. Get your 30-day Free Trial started today!
Redmine - Flexible project management web application
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.
Trac - Trac is a project management and bug/issue tracking system. Provides an interface to Subversion and an integrated wiki.
TargetProcess - Agile Project Management Web Application