I'd like to post-process log files and extract node data and transitions, and then graph them in a gui of some kind. So, I'd like to programmaticly draw bubble diagrams, maybe with animations showing packets going from node to node.
Ideally, perl or java would be the language of choice, but anything that runs on a linux platform would be fine.
What is the best library for this kind of thing?
Java Solutions
Two possibilities in Java include Prefuse and Visual Library. They both have the ability to display graphs with some animation ability. Prefuse has better graph layouts. Visual Library is more Swing-like if you are used to Swing development.
Adobe Flash
If you are willing to work with Adobe Flash, Flare is probably a little more suited to your task as it has better animation capabilities and has good graph layouts.
Animation Libraries
If your diagrams are fairly simple, you could create your own diagrams and use the Timing Framework or Trident for animation.
Other
Some other possibilities include Processing and JavaFX. Javascript libraries include ProcessingJS and Protovis.
If you can convert the output into graphviz dot format (graphviz) than you can use idot incremental viewer (iDot_incremental_viewer) which uses prefuse behind the scenes and it's completely free. The only thing you need to do here is to convert the output in simple dot file. Rest will be taken care of incremental viewer.