Red John can be seen in the season finale that Patrick Jane shoots the false Red John.
He is the guy with the red shirt wearing the black cap (he seems to be fond of wearing baseball hats). You can see him at the mall, in the background many times. He is talking to the coffee girl, the fake red john stares at him directly while walking away just before Patrick shoots him (off screen). He also is seen running from the same place the cop (the one that gets killed in the bathtub) comes from at the end (again off screen). I am sure this is him. Who wants to bet.
