This is a very interesting topic; and generally there are LOT'S of schools of thought with regards to this.
In my opinion there isn't a place that an application
should go but rather there are generally accepted practices for the different distro's out there.
Even with these, its very much a personal choice; I for example choose to compile and install my apps to a specific directory structure that I understand well - and is completely different to what people using Fedora normally would do