the InfoVisu group at CWI provides a good overview, and many links to papers, software, and general information on the topic http://www.cwi.nl/InfoVisu/
see also: Information Visualisation
Seems to be a way to create the graphs once you know how they should look. Flowcharts, etc. The one used for various FoAM diagrams, it seems. Open source, Educational licence.
“Gephi is the leading visualization and exploration software for all kinds of graphs and networks. Gephi is open-source and free.”
“Prefuse supports a rich set of features for data modeling, visualization, and interaction. It provides optimized data structures for tables, graphs, and trees, a host of layout and visual encoding techniques, and support for animation, dynamic queries, integrated search, and database connectivity.”
Tulip software is a system dedicated to the visualization of huge graphs (GPL) http://www.tulip-software.org