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Scapple - Scapple is an easy-to-use tool for getting ideas down as quickly as possible and making connections...
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.
Linked Ideas - A macOS/iOS apps to treat ideas as links of concepts.
Xmind - Xmind is a brainstorming and mind mapping application.
OmniOutliner - OmniOutliner is a writing app for collecting information, outlining ideas, adding structure to any sort of writing.