Linked Ideas - A macOS/iOS apps to treat ideas as links of concepts.
draw.io - Online diagramming application
Xmind - Xmind is a brainstorming and mind mapping application.
PlantUML - PlantUML is an open-source tool that uses simple textual descriptions to draw UML diagrams.
vym - VYM (View Your Mind) is a tool to generate and manipulate maps which show your thoughts.
Dot Chart - Dot Chart is simple and quick online process mapping system.