Is there a way to make my knuckles harder, so if I punch someone I get less hurt and they get more hurt. Or if I miss and hit a rock the odds of breaking my knuckles is decreased? Is this possible, and if so, what exercises can I do to make them like this?
Knuckle pushups. Do it the correct way with only the first two knuckles in contact with the floor. If it's too difficult, start by maintaining a static push up 'up' position. This conditions your knuckles and your wrists.
Classic makiwara (Japanese striking post) training. It's basically a flat plank wrapped in coarse rope and bolted to the floor. Punch it repeatedly.