A very cool application to make graphs

Graphviz - Graph Visualization Software uses a language called "dot" to create graphs. If you have Windows, you can get the latest. If you have Leopard (Mac OS X 10.5) you can get pixelglow | graphviz. If you have an earlier version of OS X you have to settle for Graphviz 1.13 (v16), which is still pretty cool.