Wireflow - Create beautiful flowcharts
Freeplane - Freeplane is a powerful and free software for building mind maps.
Vexlio - Instantly create precise, beautiful diagrams
Linked Ideas - A macOS/iOS apps to treat ideas as links of concepts.
Zen Flowchart - The simplest tool to create flowcharts
vym - VYM (View Your Mind) is a tool to generate and manipulate maps which show your thoughts.