Freeplane - Freeplane is a powerful and free software for building mind maps.
Workflowy - A better way to organize your mind.
Linked Ideas - A macOS/iOS apps to treat ideas as links of concepts.
Dynalist - Dynalist is a web app that lets you break down and organize your thoughts in the format of lists.
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.
Visual Understanding Environment - Visual Understanding Environment (VUE) is a mind-mapping and concept-mapping tool.