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.
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.
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.
FeatureMap - FeatureMap story mapping, simple and effective realtime collaboration and collective intelligence tool.