You could do this, but you will need to use RocketLauncher and alternate emulators to do it.
Just create a system called Favorites or whatever you want and then create a database as usual, but then for each game you will need to point it to the correct emulator/rom name.
It is a long and meticulous job that needs to be done manually (database,media etc) , so if you have a lot of games it's going to take a loooooongggg time, plus maintaining it as well.