Interesting, do you need to go into the emulator setting so it can run that way, or what do you need to do?
Might not be the best example, but MameUI can be run from the commandline just like mame (even though the whole perpose of mameUI is the GUI "front end" it tagged on).
So "
mameUI32 arkanoid" works the same as "
mame arkanoid". And all the mame CL options work the same for mameUI: "mameui32 arkanoid -mouse -nojoystick -norotate" will force the mouse to work, disable the joystick and prevent the game from rotating, overridding how arkanoid was set up in mameUI's game specific settings.
In short, most emus will start with the form "
emuname gamename". The exact form may differ though, and the the exact option are different between emus.
Heck, you can load a word file from the commandline:
winword fullfilename (assuming you're in the folder, or word in the the path, and the filename includes the extention of ".doc" or whatever it is now).