Linked Ideas - A macOS/iOS apps to treat ideas as links of concepts.
OmniGraffle - OmniGraffle is for creating precise graphics like website wireframes, an electrical system designs, or mapping out software class.
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.
PlantUML - PlantUML is an open-source tool that uses simple textual descriptions to draw UML diagrams.
Xmind - Xmind is a brainstorming and mind mapping application.
yEd - yEd is a free desktop application to quickly create, import, edit, and automatically arrange diagrams. It runs on Windows, Mac OS X, and Unix/Linux.