My employer is a large Swiss Telco. We have many Systems used to transfer data for different tasks, e.g. Performance Management, Fault Management, Configuration Management etc.
In order explain to "Management" (pointy haired, and other) how these systems interact, I collected information about data flow/formats/protocols into a "database" ( of the comma delimited persuason) and then generated code for Graphviz (http://www.graphviz.org/) and Yed (http://www.yworks.com/en/products_yed_about.html) to visualize these Graphs.
Showing these graphs generated from my DB was rather effective at first .. but adding new systems/data flows causes both Graphviz and Yed to re-layout the graphs, since that is how they work ... Naturally this really confuses anyone trying to match that graph seen yesterday, to the graph shown today.
How would you display/layout Data-Flow between Enterprise Applications?