Workflowy - A better way to organize your mind.
Freeplane - Freeplane is a powerful and free software for building mind maps.
Dynalist - Dynalist is a web app that lets you break down and organize your thoughts in the format of lists.
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.
Visual Understanding Environment - Visual Understanding Environment (VUE) is a mind-mapping and concept-mapping tool.