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.
UX Flow Wireframe Prototyping System - Create beautiful user flows prototypes for your next project
vym - VYM (View Your Mind) is a tool to generate and manipulate maps which show your thoughts.
draw.io - Online diagramming application
Freeplane - Freeplane is a powerful and free software for building mind maps.
yEd - yEd is a free desktop application to quickly create, import, edit, and automatically arrange diagrams. It runs on Windows, Mac OS X, and Unix/Linux.