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.
Innoslate - Innoslate is a complete product lifecycle management tool integrated with systems engineering, program management, and product design capabilities.
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.
Jama - Jama combines requirement management software with enterprise collaboration capabilities to solve product delivery problems.
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.
rmtoo - rmtoo is a free and open source requirements management tool.