The main binary can be used to launch games from the command line, without invoking the GUI. For example, if you installed MAME OS X in /Applications, then the main binary is at:
/Applications/MAME OS X.app/Contents/MacOS/MAME OS X
Any preference can be passed as options to this executable. For example, you could launch Ms. Pac-Man using the following command:
MAME OS X -Game mspacman
Here are some common options: