I'm not familiar with Mamehooker, but the first thing I'd try is to launch a second instance of Mamehooker. This might require doing a second installation, to a second directory. Some programs you can do that with, some programs you can't.
I've actually toyed around with the idea of writing a app/plugin that would display the control panel/instructions(For consoles) and even a list of special moves to a third monitor, but interest seems pretty low in it so I haven't pursued it (Especially since it involes me buying a second monitor).
The other idea I've toyed with is a touchpad and a wi-fi built in, setup an app on the computer and the touchpad, and then broadcast the game to the touchpad which would then display the above. Might actually be a cleaner solution, since 3rd monitors in this configuration tend to be those RGB or USB models which introduce problems.