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Linked Ideas - A macOS/iOS apps to treat ideas as links of concepts.
vym - VYM (View Your Mind) is a tool to generate and manipulate maps which show your thoughts.
Xmind - Xmind is a brainstorming and mind mapping application.
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.
FreeMind - FreeMind is a premier free mind-mapping software written in Java.
Pencil Project - Single-user mockup / wireframing / diagramming tool