Visual Understanding Environment - Visual Understanding Environment (VUE) is a mind-mapping and concept-mapping tool.
Freeplane - Freeplane is a powerful and free software for building mind maps.
PMM - Personal Memory Manager - Personal Memory Manager helps you spin-off from the top: manage your own knowledge and ideas.
Linked Ideas - A macOS/iOS apps to treat ideas as links of concepts.
Flying Logic - Highly visual software for planning support used by strategists, process improvement specialists, teachers, and writers. Windows, Mac OS X, and Linux.
vym - VYM (View Your Mind) is a tool to generate and manipulate maps which show your thoughts.