Here's a few examples of Information Architecture flow diagrams that I've done over the years.
Tecplot data import wizard
Wizard for importing data into a scientific visualization tool for parametric analysis:
ESP Simulation platform launcher
Overview of the pages for a simulation platform. "Change conditions" is actually another whole complex flow in itself.
Because this application was actually a number of different applications working together, I also marked out which parts would be in-the-box, which we would be providing hooks for, and which would be created externally but displayed within the Launcher:
Because the training process varied depending on whether you were in practice mode or taking a test (namely if you got to change the settings) and whether you were using a full-motion simulator or a laptop, I did simple flow diagrams to show those differences:
Solucient Market Planner
An early flow diagram for a web-based data mining application (the final product was more complex than this):