Visual Understanding Environment - Visual Understanding Environment (VUE) is a mind-mapping and concept-mapping tool.
Freeplane - Freeplane is a powerful and free software for building mind maps.
Protégé - Protégé is a free, open source ontology editor and knowledge-base framework.
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.
3D Topicscape - 3D Topicscape is a Personal Information Manager that provides a template loosely based on...
vym - VYM (View Your Mind) is a tool to generate and manipulate maps which show your thoughts.