While gearing up on a content management project, a few developers were wrangling with how to share solution diagrams between Visio and OmniGraffle. While there is a level of compatibility between the two, its not ideal. While researching, I went off into a related tangent, a cross platform tool that I can manipulate from a text editor or programming language, and ended up reading about Graphviz.
Graphviz - command line tool and DSL (dot) to define and render graphs and diagrams.
Doesn't sounds like much, but check out this magic: Visualizing traceroute output with Ruby and Graphviz or how about Maven based dependency graphing?
I think prefuse (with the unbelievable looking flare) is an excellent related toolkit to look into next (interaction and animations!!!!!) .
O'Reilly: An Introduction to GraphViz and dot
O'Reilly: Graphviz - Why draw when you can code?
Orgmode.org: org-exp-blocks.el: pre-process blocks in org-mode files in Emacs to generate diagrams - rocking!
Bernt Hansen's fantastic Org Mode - Organize Your Life In Plain Text! is a working example of the above org-mode use case (and a great org-mode tutorial)
Forever for Now: UML Diagrams Using Graphviz Dot
Haven't read or experimented with yet, but will...
Linux.com: Create relationship diagrams with Graphviz
IBM developerWorks: Visualize function calls with Graphviz
Graphviz Resources - large list of viewers, navigators, language bindings, etc
WikiViz: A large list of related tools and libraries
ZGRViewer: a Java-based desktop GraphViz/DOT Viewer - Adds interactivity to viewing a dot defined graph.
Graphviz Eclipse plug-in
pydot
NetworkX
UMLGraph
