I used to think that Bob Kirkland was Red John, even before seeing season 5, but I am now leaning toward the theory that Ray Haffner is Red John and Bob Kirkland is his right-hand man.

Visualize:  Haffner is a member of Visualize.  It is without question that Visualize is at the heart of things, especially given the Red Barn episode.  Haffner is the right age to have painted the smile face on the red barn, and notably did not answer Lisbon when asked if he was there at that time.  If I am remembering correctly, I believe that Ray evasively answers her question with a question.

Name:  Also interesting, is the fact that the name Ray ... is very close to the name Roy, which is Red John's alias.

Lisbon's Dream:  In the 2nd episode of Season Six, it is noteworthy that, in Lisbon's dream, although many appear guilty, there is only one that tries to cut her with a knife ... Ray.

Nurse: When the nurse looks for another patient in Lisbon's room, it is not coincidence.  There would be no reason to put it in the script ... it does not have anything to do with the plot, in a direct way.  Therefore, the audience must come to the conclusion that Lisbon is being watched ... Why?  The only reason could be to tell Haffner (who is the next visitor) when he can visit her alone.

Is Ray Haffner Bret Stiles Son? One thing I have also wondered is if it could be possible that Haffner is the son of Bret Stiles.  With the cult Visualize, it is entirely possible that a son would not necessarily bear Bret's name and would certainly add to the drama, as well as the power that Red John has.  It would also account for how Ray (if he is RD), could be so powerful.  They also both have a similar eye color.  Just a thought ...