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