Cytoscape - Cytoscape Official Web Site
Dia - Dia is a GTK+ based diagram creation program for GNU/Linux, MacOS X, Unix, and Windows, and is released under the GPL license.
Polinode - Polinode is a tool that makes it easy to perform powerful network analysis.
Graphity - Graphity is a diagram editor that can be used to quickly and effectively generate drawings and to...
Gephi - Gephi is an open-source software for visualizing and analyzing large networks 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.