- GraphViz is maybe the most venerable.
- NetworkX is a pretty cool toolkit for Python. Very easy to use, a great starting point.
- D3's Network Graph can do some nice things, well integrated into web pages.
- Graphs and Networks in Mathematica. I have used a couple of different approaches in Mathematica, including just treating the graph as a variable. I should dig out examples; I wasn't fully happy with what I managed with simple code. But if you're willing to go through the syntactic pain, you can do amazing things in Mathematica.
- OmNeT++ and ns-3 are full-on (classical) network simulators we have used for some sims, and they have built-in or add-on visualization tools.
Do you have a favorite or a dislike among this list? What have I missed?
