That depends upon what you want to modify.
Occasionally for the handheld emulators with different (lower) resolution screens to the console being emulated we have been seen to change the text position and font style so it works with scaling, cropping and whatever else is done. Variations on that theme are common enough.
To do it for a normal 2d game... trying to do it like you would for the 3d stuff... no. I had contemplated something like an emulator that freeze frames, manually shifts the camera so the game takes care of the rest and then the emulator stitches it all together, obviously things like random battles, cutscenes and more would break the effect at times but at others it would work I guess. I would sooner remake a game than try to hack it into a 2d game from the SNES or something like the SNES (basically everything that is not doing 2d off the back of a 3d engine).
For 3d then yeah the bigger part of such hacks is getting the game to work properly -- I was not kidding when I said the enemies might only be rendered and that leads to them popping in, the floor might only be in what the game "normally" sees and that is in addition to the animation and game event trigger stuff.
See something like
That is not bad actually but see where the fade only applies to the original 4:3 stuff? That is just the tip of the iceberg.
Another might be
Though I should note that much of this has been worked upon.