GraphViz

GraphViz - Graph Drawing Tools: "Graph drawing is a way of visualizing structural information as diagrams of abstract graphs and networks. Automatic graph drawing has many important applications in software engineering, database and web design, networking, and in visual interfaces for many other domains.

Graphviz is open source graph drawing software. It has several main graph layout programs. See the gallery for some sample layouts. It also has web and interactive graphical interfaces, and auxiliary tools, libraries, and language bindings."
Theory