UXpin - Design is really about solving problems. UXPin is the UX Design Platform that gets that right.
Freeplane - Freeplane is a powerful and free software for building mind maps.
Moqups - The most stunning HTML5 app for creating resolution-independent SVG mockups, wireframes & interactive prototypes for your next project
Linked Ideas - A macOS/iOS apps to treat ideas as links of concepts.
Axure RP - The prototyping and specification software used by 87% of the Fortune 100. Beyond mockups, design interactive prototypes for business solutions, websites, and applications.
vym - VYM (View Your Mind) is a tool to generate and manipulate maps which show your thoughts.