It may be that I'm just not a visual person, but I'm currently working on a project that has a large visual component in Pentaho Data Integrator (a visual ETL tool). The top level is a pretty simple picture of six boxes in a pipeline, but as you drill down into the components the complexity just explodes, and it's really easy to get lost. If you have a good 3-D spatial awareness it might be better, but I've started printing screenshots and laying them out on the floor. I'm really not a visual person though...
