Cytoscape - Cytoscape Official Web Site
Gephi - Gephi is an open-source software for visualizing and analyzing large networks graphs.
Polinode - Polinode is a tool that makes it easy to perform powerful network analysis.
Visallo - Visallo helps intelligence analysts, law enforcement detectives, and fraud investigators produce...
Prefuse - the prefuse visualization toolkit
KeyLines - The JavaScript toolkit for graph visualization