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vym - VYM (View Your Mind) is a tool to generate and manipulate maps which show your thoughts.
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.
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
Marked - Marked takes Markdown text–a simple syntax you can learn in minutes–and turns it into beautiful...