Clues to what, exactly? All PPC-only applications do not work with Lion or Mountain Lion. There are only a handful of applications that the installer "knows" do not work with Lion or Mountain Lion. Hence, the use of the word "known." You will find a more complete list at App Compatibility Table - RoaringApps - App compatibility and feature support for OS X & iOS.
If you have PPC-only applications they should be removed or upgraded.
I'm fully aware that PPC apps do not function with Lion or Mountain Lion.
The question was/is: Why don't the migrating PPC applications end up in a folder at the root level of the Mountain Lion volume titled "Incompatible Software." Instead, one must manually feret out all old PPC applications and supporting files for trashing.
As I stated. They are not in the installer's list of known incompatible applications. Most likely because there are just too many of them to keep track of. PPC-only applications have been out of the picture since 2006. PPC stuff should have been fereted out before starting with Lion or Mountain Lion. They should have been handled when the user switched to Intel hardware. It's not like this is something that's only come to the surface.
The installer doesn't isolate a lot of stuff that's incompatible. But Apple does make suggestions that one remove or upgrade their software if it is not compatible BEFORE upgrading. Perhaps you need to pass that information along to your clients ahead of time. Or do an erase and install then reinstall only third-party software that is known to be compatible.