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PMM - Personal Memory Manager - Personal Memory Manager helps you spin-off from the top: manage your own knowledge and ideas.
Freeplane - Freeplane is a powerful and free software for building mind maps.
Visual Understanding Environment - Visual Understanding Environment (VUE) is a mind-mapping and concept-mapping tool.
Linked Ideas - A macOS/iOS apps to treat ideas as links of concepts.
Rationale - Rationale let's you create, online, argument maps.
vym - VYM (View Your Mind) is a tool to generate and manipulate maps which show your thoughts.