Gephi - Gephi is an open-source software for visualizing and analyzing large networks graphs.
Dia - Dia is a GTK+ based diagram creation program for GNU/Linux, MacOS X, Unix, and Windows, and is released under the GPL license.
Wandora App - Wandora is a general purpose information extraction, management and publishing application based on...
draw.io - Online diagramming application
Linkurious - Search and visualize your graph data through a simple web-based interface
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.