Invision - Prototyping and collaboration for design teams
vym - VYM (View Your Mind) is a tool to generate and manipulate maps which show your thoughts.
Balsamiq - Balsamiq. Rapid, effective and fun wireframing software.
Linked Ideas - A macOS/iOS apps to treat ideas as links of concepts.
Moqups - The most stunning HTML5 app for creating resolution-independent SVG mockups, wireframes & interactive prototypes for your next project
Freeplane - Freeplane is a powerful and free software for building mind maps.