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.
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.
OmniOutliner - OmniOutliner is a writing app for collecting information, outlining ideas, adding structure to any sort of writing.
Freeplane - Freeplane is a powerful and free software for building mind maps.
Pencil Project - Single-user mockup / wireframing / diagramming tool