I like the knuckle pushups because you get an extra three to four inches before your chest hits the floor. Plus, the supportive muscles of the wrist have to work(isometric contraction) in order to keep your wrists from buckling. That is a good thing for punches. You don't want your wrist to buckle in a punch. I like to change around my fist position to work muscles differently, such as:
In-line wide (fists in line with each other as if you're holding a barbell during bench press, with wide grip a little more than shoulder width apart) This is good specifically for the chest, and your elbows should go out to the sides.
Opposite narrow (fists opposite of each other as if you're holding a hammer-curl bar, shoulder width apart.) This is good for the triceps, and your elbows should stay along your sides.
45 Degrees (Your fists should be at a 45-degree angle, and your elbows should also go out at 45 degrees instead of straight out or straight back.) this is good for chest, and triceps.
Of course all of these are good for the shoulders as well, but I like to mix them all up. I started doing knuckle pushups mainly because open palm pushups aggravated my wrists if I did them regularly. Now I always do knuckle pushups.