Graphviz is a graphing toolkit that allows you to render several sorts of directed and undirected graphs like this:

A CLI version of Graphviz is available for pretty much any UNIX variant under the sun.

Pixelglow has a very neat Mac OS X port of Graphviz, complete with a new document-based GUI, export to PDF and many more bitmap formats, full alpha transparency, native font support and anti-aliasing:

The dynamic zoom has to be seen to be believed, and the properties sidebar is a great way to tweak the layout. All in all, a great example of how “old school” UNIX tools can be adapted to run under Cocoa.

There is also an amazing iPhone implementation called Instaviz.