Ever since Bruno Heller mentioned a key clue in the final sequence of 6x01 (The Desert Rose), there have been many guesses as to what that clue might be. Some guesses have been the '666' on the wall, the pigeons and Partridge quoting 'Tiger Tiger'.

I don't believe that it is any of these. In my opinion, the key clue which Heller mentioned in this scene, the fact that Red John is holding the blade which he used on Partridge in his left hand. This shows that Red John is a left hander. At the time, this is relatively meaningless because it is very difficult to determine which hand all of the suspects use and if one of them is, indeed left handed.

However, at the end of 6x03 (Wedding In Red), Jane slips on the roof whilst being held hostage by the murderer and manages to cling on by his fingertips. Sheriff Thomas McAllister arrives just in time to save Jane, killing the suspect in the process. When McAllister comes to help Jane up onto the roof, he reaches down with his left hand.

This confirms that both Thomas McAllister and Red John are left handed. Given that only 10% of the population are left handed and there were only six people remaining on Jane's list at this point in time, statistically, there is only one left hander on the list. McAllister is left handed. McAllister is Red John

Also, Xander Berkeley (who plays McAllister) had eight years removed from his age for his role as McAllister. Berkeley is 58. However, McAllister is only 50. This reduces his age when the murders in the barn (The Red Barn- Season 5 Episode 13) occurred from 33 to 25. This makes it much more likely that he was the 'kid' who Talbot said drew the face on the barn.
Additionally, the actor who is suspected to play young Red John (Nick Nordella) is 25 years old and resembles a young McAllister. Why change McAllister's age to fit these criteria exactly? Because Thomas McAllister is Red John :)