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TiddlyWiki - a non-linear personal web notebook
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.
wikidPad - wikidPad is an application for storing thoughts, ideas, todo lists, contacts, or anything else that user can think of to write down.
vym - VYM (View Your Mind) is a tool to generate and manipulate maps which show your thoughts.
Knowledge Workshop - Learning Management Solutions provides innovative and reliable software for the knowledge worker.
Freeplane - Freeplane is a powerful and free software for building mind maps.