draw.io - Online diagramming application
asciiflow - Infinite ASCII diagrams, save to Google Drive, resize, freeform draw, and export straight to text/html.
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.
Core2D - A multi-platform data driven 2D diagram editor.
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.
PathVisio - Open-source and free pathway analysis and pathway drawing software. Allows drawing, editing and analysis of biological pathways.