draw.io - Online diagramming application
asciiflow - Infinite ASCII diagrams, save to Google Drive, resize, freeform draw, and export straight to text/html.
UMLGraph - UMLGraph is a professional automated drawing tool that allows the designers the declarative specification and drawing of UML class and sequence diagram.
PathVisio - Open-source and free pathway analysis and pathway drawing software. Allows drawing, editing and analysis of biological pathways.
Dia - Dia is a GTK+ based diagram creation program for GNU/Linux, MacOS X, Unix, and Windows, and is released under the GPL license.
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.