Xmind - Xmind is a brainstorming and mind mapping application.
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.
MindMeister - Create, share and collaboratively work on mind maps with MindMeister, the leading online mind mapping software. Includes apps for iPhone, iPad and Android.
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.
FeatureMap - FeatureMap story mapping, simple and effective realtime collaboration and collective intelligence tool.
Redmine - Flexible project management web application