Some fairly unnoticed points that need to be explained:

1. Why is Haffner so interested in the Red John case? He referred to a client who's interested in the case. Logically speaking there are only two possibilities, First, he is Red John and there is no client. He is not Red John and there is a client. But who is the client? Visualize? Stiles doesn't seem to be interested in the Red John case, why would Visualize be? Is the client Red John himself?

2. Of what nature was Kirkland's relationship with Bertram? They seemed to be close. Apparently Bertram is a member of the Tygers, and apparently Kirkland was after the Tygers. So was Bertram playing a role and fooled Kirkland? If that's the case why would the Tygers let Kirkland get close to Jane and the Red John case? Or was it the other way around. Or maybe Kirkland is a high-level member of the Tygers about whom only Bertram knows, and they faked Kirkland's death, Which could make it possible he is Red John.

3. How did Stiles know the whereabouts of Kristina Frye?

4. Is Rosalind trustworthy? If she is, why didn't Jane take her description
into account? If he forgot to do that then he's incompetent; if he
didn't and the producers did, then they're incompetent. If she's not
trustworthy, why did Jane ask her whether Timothy Carter was Red John or
not?

5. Is Alexas Shultz a Tyger member? If she was then why would she work for Kirkland? Would that confirm Kirkland was a high-level Tyger member? Or possibly Red John himself? If he is Red John why would he kidnap men from Jane's fake list and ask them if they're Red John?!

6. Why didn't Jane set a trap when he knew Red John was going to kill James Panzer(aka the SJK)?

And many other unanswered questions.

This might be a little too simplistic, but taking into account the following, I'd say it's Sheriff Thomas McAllister. I have a second guess - but that comes after.

1. BH says he's been there from the start. Only the Sheriff and Brett Partridge have been there from there start and well, the latter's dead. 

2. 'He is Mar'. Has everyone forgotten this writing on the wall? Call me naive, but was it supposed to write 'He is Macallister (almost dying people might not care about spelling)?' 

3. RJ was 18-30 years old when he worked in the Elliston Farm, the Sheriff seems about just the right age.  

4. Lastly, which has nothing much to do with the show but more the actor, Xander Berkeley would be THE PERFECT candidate to portray Red John. If you watch Nikita (where he played Percy), you'd feel as strongly as well. A psychotic, sadistic yet polished individual with a deep-rooted evil within him. I always pictured Xander Berkeley coming out of the Sheriff outfit and into a sleek suit, revealing himself as RJ.

The only thing that throws me off is the phobia which Sophie Miller mentions. 'Acrophobia', fear of heights. I've replayed that scene many a time and it is very clear she says 'Acrophobia' and not 'Arachnophobia' - which I initially read another theory about this possibility. However, in 6x05, it is revealed to us that Haffner does indeed have Arachnophobia (the scene with him, Lisbon and Van Pelt where he freezes at the sight of a spider). You gotta ask yourself, what the hell does that have to do with anything? At this point in the show, I don't think the writers would write in something like that just for kicks. Was this a huge clue for us, or just to throw us off? If it was a clue, then my second guess would be Haffner. He fits Rosalind's, Father Peter De Bono and Sophie Miller's physical descriptions. 

I have to say, if RJ was Bertram or Smith I would be disappointed. Bertram would be too obvious a choice (oh hai we're gonna make RJ the director of the CBI) and Smith just seems too random a choice.

And admit it, Brett Stiles is too old to be RJ. 

Whoever it is, I definitely am on the edge of my seat for the next few episodes.

Partridge = Flashback ---> Green
Partridge = Red John   ---> Red

I will be happy to see all episodes once again if Partridge is redjohn...

I like the fact that BH has kept everyone guessing from week to week, continually throwing things out that cause everyone to re-evaluate their take on who RJ is.  Like a lot of people, I thought for quite some time that Brett Partridge was RJ.  Him showing up on the list that BH confirmed in multiple interviews was legit cemented this.  Then he goes and get's offed (presumably) by RJ in episode 1 throwing that out of whack.  Since then, and in numerous ways, BH has said over and over again that the list is legit, Brett Partridge is definitely dead, and there was a reason why BP was killed when he was.

So, Brett Partridge is not just merely dead, he's really most sincerely dead.  BUT, in the face of BH continuing to confirm that BP is dead, could he really be saying that the persona of BP is dead, ie, the RJ alias Brett Partrdge is dead?  Thus he is off the hook to confirm the list is legit, throw everyone off by saying that the character many people thought was RJ is dead, and be able to come back and say that we'll be disappointed in the reveal.  A part of me thinks that BP as RJ would be a little cheesy, but at the same time I would be like, "YES!  Nailed it!!"

I don't recall BH ever expanding on his statement that BP is dead, so BP as a persona that RJ "killed off" is completely in the realm of possibility.