Not a real theory, just my opinion about the whole McAllister affair after he was announced dead in the recent episode, even though he stood on the 'safe' side of the house in 6x06.
This fact resulted in a whole lot of theories that he is alive and he is Red John. I just can't understand that. Here's why:
http://www.youtube.com/watch?v=M9tR57B9jWE
In the scene, we can see and hear the shot @2:23. After the shot, we still see the house for like 1 second before the scene changes. That means the explosion did not happen at the same moment as the shot.
The explosion happened at least 8 seconds later. Because in 3:10 there is Lisbon running towards Jane's house and we don't hear any shot. In 3:18 there house explodes. During those 8 seconds (probably more), ANYTHING could happen in the room. There could be a fight, someone could have tried to escape, and all positions could switch within very short time. So there's nothing special about the fact that McAllister is dead. You can tell that Stilles or Haffner are alive and the probability is the same.