Other than Mega Maker, there is no one program or method, Unlimited was made in Game Maker, which is the most common way other than rom-hacking, but there are indeed a LOT of Freeware Maga Man games, Day in the Limelight 1 & 2, Revolution, Rock Force, Super Fighting Robot, 2.5D and more.
Though, a quick search for Mega Man Game Maker DID reveal what I already suspected, that there indeed is Mega Man Canned Software:
And the comments reveal that there were others predating this (though supposedly not as good)