Software used in this project

Cichlid
An OpenGL visualization library, BSD license. Very clean and nice C code. Discontinued in 2001. Its currently the main visualization engine of glay.
Gem
An extremely fast layout algorithm. Very bright ideas, sometimes not quite clear nomenclature in the code. We definitely learned a lot from them, and also cut-and-pasted the heart of their code, so the "Gem" layout algorithm is available.

Software in the area

Pajek
A popular MS Windows based graph visualization and layout binary. Easy to use, solid. Free for academical use, but not open source, so you've got to live with its flaws. One of them was (maybe its not anymore, it was in 2002) that you couldn't use rgb for the colors, just a 16 color palette.
GraphViz
A comprehensive, solid software suit for handling graphs. They have a much better collection of resouces than this one.
Lemon
A well designed, powerful graph algorithm library. Heavily templated C++. Its main objective is to implement all known algorithms used in operations research.