I use whiteboarding too, but yeah, it's basically a snapshot / dump of institutional knowledge that resides in an individual's head. Updated my post to mention that I'm looking for something electronic / scalable
I want to avoid the situation where the left hand doesn't know what the right hand is doing. Any person on the team doesn't have to go hunt down the person who knows the system, but can just look up the diagram at a high level and know where to start.