CPN Tools has been used for modeling everything from garbage waste disposal plants to communications protocols. It is based on state machine theory and is an extension of place-transition Petri nets. The tool is in use by hundreds of commercial, government and academic organizations around the world. The university does a very credible job of maintaining the product and keeping the updates coming.
I have used this tool to model the behavior of the SQL slammer worm on a large multinational network. I have a colleague who has used CPN Tools to model and simulate the behavior of attacks across the internet. The bottom line is that this tool is great for figuring out how something will behave on your network. A good example is figuring out how the addition of a new network device, such as a web server, will impact the security of the network. CPN Tools not only lets you model the network and its behavior, you can run the simulator when you've finished with the model to see what the behavior will look like.
The tool is completely graphical which makes it very easy to use - you don't need to understand all of the underlying modeling math - and the simulator makes a dramatic demonstration for laypeople. Using a tool called BRITNeY Suite, you can add animation to the nets, making them even easier for a lay audience to follow.
CPN Tools is not an analyst tool for everyone, but for those security engineers who need to understand the behavior of their networks in more depth or are designing new networks that need solid security, this could be just the thing. And the price certainly is right.