Graphviz is the "market" leader, lots of papers and research into grap drawing on that website too. There is a python module to generate dot files.
Networkx is a python module that uses different "backends" to do the drawing, matplotlib and graphviz mainly, claims to handle 10M+ edges and nodes, must try this as graphviz falls over with my facebook data.
This is what wikipedia thinks about it.
Processing
The processing environment is geared towards animations, images and such. The Visualizing Data book uses processing.