Morph targets are generally preferred for animating mouth movements, but especially for lip syncing in anim8or. Other programs have different forms of morph targets or something of the sort, but from what I've seen, bones usually aren't preferred for animating mouths.
Bones are normally preferred for skeletal type movement, or normal movement upon a hinge. The jaw does move on a hinge, but there is lip movement as well which makes things much trickier and not preferred with bones. Therefore you use morph targets. So when animating things such as a mouth, a piston, or even something like a flag you may want to use morph targets. When animating things such as a hinge, or a character bones would be preferred. You can get smooth transitions with bones as well, such as a rope, though you use many bones in a line normally to give more freedom.
I hope that helps you a bit
