Normally, you place game ROMs under the public (or user_) games folder, in the appropriate game system folder.
There _ARE_ physical cartridge and controller interfaces. The http://www.retrode.org/
is the best example of one. It provides a virtual disk that can be seen to have ROMs that can be read by the emulators. I do not have one yet, but as soon as I get one (and some carts), I will try to make fully integrated support for it.