POP (Prototyping on Paper) - POP helps you make interactive prototype with ease. If you can draw, you can design apps.
UX Flow Wireframe Prototyping System - Create beautiful user flows prototypes for your next project
Marvel - Turn sketches, mockups and designs into web, iPhone, iOS, Android and Apple Watch app prototypes.
draw.io - Online diagramming application
Balsamiq - Balsamiq. Rapid, effective and fun wireframing software.
yEd - yEd is a free desktop application to quickly create, import, edit, and automatically arrange diagrams. It runs on Windows, Mac OS X, and Unix/Linux.