Workflowy - A better way to organize your mind.
Xmind - Xmind is a brainstorming and mind mapping application.
Dynalist - Dynalist is a web app that lets you break down and organize your thoughts in the format of lists.
MindMeister - Create, share and collaboratively work on mind maps with MindMeister, the leading online mind mapping software. Includes apps for iPhone, iPad and Android.
SuperNotecard - Introducing SuperNotecard. SuperNotecard is an online writing tool that features virtual notecards to help arrange facts or scenes, track details, organize paragraphs, and clarify your composition process.
Coggle - Coggle is a simple, beautiful, powerful way of structuring information.