Cytoscape - Cytoscape Official Web Site
UCINET - UCINET for Windows is a software package for the analysis of social network data.
Polinode - Polinode is a tool that makes it easy to perform powerful network analysis.
Gephi - Gephi is an open-source software for visualizing and analyzing large networks graphs.
Graphviz - Graphviz is open source graph visualization software. It has several main graph layout programs.
Linkurious - Search and visualize your graph data through a simple web-based interface