quickMockup - Online tool for creating mockups in the browser.
SuperNotecard - Introducing SuperNotecard. SuperNotecard is an online writing tool that features virtual notecards to help arrange facts or scenes, track details, organize paragraphs, and clarify your composition process.
POP (Prototyping on Paper) - POP helps you make interactive prototype with ease. If you can draw, you can design apps.
vym - VYM (View Your Mind) is a tool to generate and manipulate maps which show your thoughts.
Invision - Prototyping and collaboration for design teams
Freeplane - Freeplane is a powerful and free software for building mind maps.