Useful Graph and Network Analysis Tool

Gephi: https://gephi.org/
iGraph: http://igraph.sourceforge.net/
NetLogo: http://ccl.northwestern.edu/netlogo/

Other tools
pajek: http://vlado.fmf.uni-lj.si/pub/networks/pajek/
NetworkX: http://networkx.github.io/
NodeXL: http://nodexl.codeplex.com/