Dia - Dia is a GTK+ based diagram creation program for GNU/Linux, MacOS X, Unix, and Windows, and is released under the GPL license.
JFLAP - JFLAP is software for experimenting with formal languages topics including nondeterministic finite...
draw.io - Online diagramming application
GraphThing - GraphThing is a tool that allows you to create, manipulate and study graphs.
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.
Gephi - Gephi is an open-source software for visualizing and analyzing large networks graphs.