Freeplane - Freeplane is a powerful and free software for building mind maps.
ConnectedText - ConnectedText is a powerful but simple information management system.
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.
TiddlyWiki - a non-linear personal web notebook
vym - VYM (View Your Mind) is a tool to generate and manipulate maps which show your thoughts.
Ultra Recall - "Ultra Recall is personal information, knowledge, and document organizer software for...