Are there any apps that can show the final configuration as applied to a particular application directory? What I'm picturing is something along the lines of FireBug's CSS viewer.
Basically, it should show the equivalent single web.config file (as if you only had one), with all the values that apply to the directory in question, with each element (or even attribute) annotated with its source (the real .config file it came from).
This would greatly help deploying applications into foreign environments (eg, customer sites) where they sometimes have strange configs, that add in global includes (eg, they put the include in machine.config, instead of the web.config for that app) or have allowOverride=false, etc.