Actually, there are lots of other games that are hacked. Before starting my Project (unannounced here yet) I worked on Many Super Mario World Hacks. I mean, lunar magic, that's almost every tool you would need to hack (and most only used it) right in one. Also, Fire Emblem, Megaman, Mario Bros. 3, Super Mario Bros, Zelda, Zelda A link to the past, the genesis/mega drive sonic games get hacked a lot too.
But, Super Mario World and Pokemon are by far the most hacked games, mainly cause it's the easiest. Plus, Pokemon is here cause it's a pokemon community.