Application CFMs can be used where ever you want to tailor the application scope's use.  If you want to extend the length of the session scope for example, a modified application CFM can be placed in the role (screen) folder that you want to modify and anyone who navigates there will get a new scope with a longer session time.  One drawback to this is that you need to maintain that application scope. separately.  It would be nice if you could use inheritance to make management easier and more consistent.

There are several benefits to using application.cfc as a replacement for application.cfm.  Using a CFC's ability to inherit from another seems like a nice way to keep all those custom session lengths under control.

In our implementation we set up our application at the root of the module and in the role that needs an longer session we inherit the root application.cfc and set the sessiontimeout.