LucidChart - LucidChart is the missing link in online productivity suites. LucidChart allows users to create, collaborate on, and publish attractive flowcharts and other diagrams from a web browser.
UX Flow Wireframe Prototyping System - Create beautiful user flows prototypes for your next project
Moqups - The most stunning HTML5 app for creating resolution-independent SVG mockups, wireframes & interactive prototypes for your next project
draw.io - Online diagramming application
OmniGraffle - OmniGraffle is for creating precise graphics like website wireframes, an electrical system designs, or mapping out software class.
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.