Completed: Eight Sweets, The Heart of Tales, [redacted] Life, Must Love Jaws, A Tune at the End of the World, Three Guys That Paint, The Journey of Ignorance, Portal 2.5.
I know Trello is used a lot for collaborative indie game projects. I've used it before on several collabs, and it has some useful widgets (you can attach images, screenshots, docs, etc.)
CmapTools is a good (and free) mindmapping software. You may also want to consider using Google Docs to create a diagram instead, as Trello allows you to directly attach Google Docs to its (Trello's) site for easy group access.
I really enjoy using yEd graph editor, as you can be as messy as you want and with a click of a button it will organize everything into pretty hierarchies.
