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.

“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