Overflow.io - User flows done right
draw.io - Online diagramming application
Invision - Prototyping and collaboration for design teams
UMLGraph - UMLGraph is a professional automated drawing tool that allows the designers the declarative specification and drawing of UML class and sequence diagram.
FlowMapp - FlowMapp is a UX planning tool for creating visual sitemaps and user flow.
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.