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Linked Ideas - A macOS/iOS apps to treat ideas as links of concepts.
Freeplane - Freeplane is a powerful and free software for building mind maps.
vym - VYM (View Your Mind) is a tool to generate and manipulate maps which show your thoughts.
OmniOutliner - OmniOutliner is a writing app for collecting information, outlining ideas, adding structure to any sort of writing.
Pencil Project - Single-user mockup / wireframing / diagramming tool
Visual Understanding Environment - Visual Understanding Environment (VUE) is a mind-mapping and concept-mapping tool.