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Dynalist - Dynalist is a web app that lets you break down and organize your thoughts in the format of lists.
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.
Workflowy - A better way to organize your mind.
vym - VYM (View Your Mind) is a tool to generate and manipulate maps which show your thoughts.
Indigrid - Plain text outliner with side-by-side views.
Freeplane - Freeplane is a powerful and free software for building mind maps.