Easy to solve, really
Cisco came out with Tetration, which can totally solve the "what the heck is my app talking to?!?" part of this issue. I saw it take a two year data center mapping project (which really means it would never be current and accurate) and finish it off in two weeks. As long as the dependencies occur within the time window you're observing, you'll have it totaly mapped. (you'd miss connections for a monthly report run, for example, if it didn't occur for you to observe)
Its' a little (a LOT) spendy for small shops today, but there will be far more affordable, smaller-scale options in the very near future. The things it can do sound unbelievable, but it works. Works well without Cisco based networks if you're the adventurous type who prefers buying tech from the "Other vendors" wedge on the market share pie chart. Of course it works even easier/faster/better with Cisco gear if you prefer to have widely available, supportable tech for which you can easily hire more engineers running your production network. (I'm a success bigot, not a Cisco bigot :) )
Biting the hand that feeds IT
