LucidChart - LucidChart is the missing link in online productivity suites. LucidChart allows users to create, collaborate on, and publish attractive flowcharts and other diagrams from a web browser.
Freeplane - Freeplane is a powerful and free software for building mind maps.
draw.io - Online diagramming application
Linked Ideas - A macOS/iOS apps to treat ideas as links of concepts.
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.
vym - VYM (View Your Mind) is a tool to generate and manipulate maps which show your thoughts.