I see it happening, probably in two iPhone/iPod iterations from Apple depending on the success of the 3DS. 3D video would look great even if games don't, and even so many games simply use virtual buttons that float above the screen. With 3D enabled they would just...float more. I don't see it being a problem....heck, I don't see it being a problem even for game that DON'T use the virtual button method, as long as the user-controlled images are on the topmost "layer" of depth. It might be weird at first, but not insurmountable.
In any case, if 3D movies continue to be popular I can definitely see Apple wanting to sell them on iTunes, which would require some sort of device to play them. They won't let Nintendo have exclusive control over glasses-free 3D movies if that turns out to be something consumers want. And if it isn't, Apple will MAKE it something consumers want because somehow they know how to do that.