interactive visualization and exploration platform for all kinds of networks and complex systems, dynamic and hierarchical graphs. Runs on Windows, Linux and Mac OS X. Gephi is open-source and free.
Experimental PHP extension that draws inclusion graphs (showing which files are required())
sequence diagrams of several protocols in PDF
open-source UML tool with a simple user interface: draw UML diagrams fast, export diagrams to eps, pdf, jpg, svg, and clipboard, shar