I realize that Ray Haffner is supposed to be dead, however for those of you who havn't been reading the news check your sites:

http://www.tvguide.com/news/mentalist-episode-recap-red-john-revealed-dragon-1073521.aspx?fb_action_...

So in truth nobody can really be confirmed dead except for Partridge, if he is not dead then they better have a good explanation as to why Cho didn't notice anything.

DNA evidence does not confirm the deaths of Haffner, Stiles, or Mcalister as any of these could be planted or interpreted by Association members.

So my theory is that Bertram is and has always been the leader of this secret society and Red John has been a fly in the ointment that has infiltrated it at some point or another.  Who knows how Red John infiltrated it.  I think it is unlikely he is a member as they would be controlling him, its more likely that one of his disciples happed to be a member and he came across it that way, and by controlling a few of them he controls enough of the Association to suite his needs. 

At this point Bertram is on the run because of the secrets in his past that he doesn't want revealed, as well as the backlash of the organization being revealed.  He has been playing a dangerous game the whole time, on the one hand he has always wanted Jane to find Red John, but only in a way in which Jane doesn't find the association.  This is why he was always carefully paired with "good cops" who had no knowledge of it.

Even so, Bertram would not have known if Ray Haffner was Red John, he would only know that Haffner wasn't  member of Tyger Tyger, this is why he still paired Jane with him in season 4. 

Logically if this theory is sound then its not Mcallister either as he is a member of the association, probably for some time.  Nor would it have ever been Partridge for the same reasons. 

The most likely candidates then would be either Stiles or Haffner.

The main reason that I like Haffner for this over Stiles is because he fits the Red Barn clues better.  Stiles would have been running visualize at the time, or at least very high up (if he was not the founder) where as Haffner was the perfect age at the perfect time to fit the crime.  The only way I see Stiles being Red John is if the Red Barn was a false clue, or if Ray Haffner was one of his early students (also unlikely)

So there you have it, I believe its Ray Haffner, mostly by process of elimination.