It will definitely be Bret Stiles.  I can only offer meta proof, no actual proof.  For one, he is the biggest star on the list of characters, and as Family Guy said, it's always the biggest star.  For two, he is the only leader of a cult-like organization and a conspiracy of this magnitude will take a cult leader to inspire it all.

Coffee. There's something about the coffee (or maybe I just need coffee). Seriously, though, when Kirkland shows up to meet with Smith, he brings three different coffee choices. This signifies a couple things, one of them being that Kirkland is "prepared." In this case, he's come prepared for variations in coffee choice, but I believe it foreshadows his "preparedness" with the Red John case. We've seen the man obsessed to find Red John several times. He's smart, and he's prepared for different outcomes. There's no way that the Kirkland we've seen depicted dies without having a "fail-safe" of sorts. His death or something he leaves behind will prove invaluable to Jane's investigation. (I still maintain that there's something strange about the "pigeon person" beside Jane and Lisbon while they're drinking coffee in 6x02!) Coffee!  I, like others, find Van Pelt's behavior odd, always have. She's always been a bit weak, except for when she shot her fiance (perhaps to prove to Red John that she is not weak?) I think, from the beginning, she's been set up as an informant of sorts. She's part of it somehow. She has always found Jane's "gift" intriguing; she also has computer skills. Lisbon also first told Van Pelt about Jane's 7 suspects. She's also the one that told Lisbon where to go to find Patridge, where Lisbon was ultimately attacked. And, I've never seen Van Pelt drink coffee, and that makes her suspicious to me. Van Pelt is the CBI insider, mark my words. With this last episode, I finally feel like we know more than Jane. We were given inside information in reference to "Tyger Tyger," which turns out to be a "password" of sorts, part of an insider coverup that involves multiple law enforcement agencies. So, when people are dying and "Tyger Tyger" is on their lips, it can only mean a couple things 1.) They feel betrayed and are offering a clue toward solving the greater mystery of Red John or 2.) It's offered as a response to something they've done, a sacrifice, or contribution toward protecting someone in authority. What makes this interesting is that we know some of the implications and significance of "Tyger, Tyger," but Jane and Lisbon do not. Knowing the implications, though, also gives us insight into Jane's positionality, where now, he appears to be more of a "pawn" than we've been lead to believe. Interesting development indeed! It's almost as if now we know that Jane and Lisbon and others have been moved around the chessboard by a master chess player. Jane and Lisbon are being used toward some endgame, but what? It's a power struggle, between two people, I think: But it's not Red John and Jane. It's between Red John and someone who believes s/he's his equal, someone who has great skills of manipulation and charisma. Red John hates competition, remember? He's let Jane live and Lisbon live; they're not the competition he fears. In fact, I'm pretty sure he feels confident that he can manipulate them any way he wants, just the way he has been... Only time will tell... I'm off to get some coffee!

Like many of us, I don't like the last episode, 6x04. The idea of a whole organization supporting murders and protecting themselves by dissimulations over some dark secrets is something that destroys the relationship that's built between Jane and Red John in the five seasons.

BUT, it gives us a clue : I have a strong feeling that Red John is at the head of this organization. This is definitly supported by the William Blake poem he told Jane about, remember :
"Who created your fearful symmetry ?" => I guess it's you, Red John.
+ This is supported by the words of Bruno Heller, comparing Mentalist to Moby Dick. They want to trap THE one that was at the beginning of the whole story, the one that was always just right behind them, and manipulated everyone. That must be the leader.

He wouldn't be able to hide his mistakes if he didn't have this bunch of minions that carry on the dirty work for him.
I bet Partridge was the one who cleaned up everytime the scene of murder before anyone else came (the reason why we saw him on approximately each murder done by Red John).

Now, think about it : if Red John is the leader ... he gives orders to the others (they do the dirty work and cover him. They're glad to do it because he is their protector, their savior), and is above them.
What we saw on 6x04 : Smith was asked to keep an eye on Kirkland from the start by Red John. When the first murder occured (Marx), RJ maybe already knew it was because of the fake list, and Kirkland was at the origin of it. If he didn't at that time, he was informed by Smith when Kirkland came to talk to him.
Smith was also asked, when Kirkland was finally trapped and could give informations to Jane, to kill Kirkland. This is not the motus operandi of Red John, who didn't hesitate to kill Partridge when this one didn't want to follow him anymore.
Smith can't be Red John.

But here come two a question : how did Smith know that the "Tiger Tiger" that Kirkland said was not the one they use in the organization ?
Three options :
- The organization is smaller than what we think, they all know each other and can recognize them => Would be weird since there are people from all ranks in it.
- People in the organization have another way to recognize them, so that they can identify the ones that use Tiger Tiger without being from the organization => Maybe, but would be complicated to introduce a late symbol again, we just happened to learn what was the meaning of the first one.
- People in the organization are only using Tiger Tiger while following the orders of their leader, Red John => Most likely a plausible option. Would make sense with the fact that, when some minions die, they only pronunce "Tiger Tiger" to lead Jane and Lisbon to the leader of the organization, the one that gives the instructions.

IF Red John is the one that gives the instructions, THEN :

- Bertram can't be Red John. His role has been defined by Red John to keep an eye on Jane in the CBI : it has been repeted by Smith, on an authoritarian tone, in 6x02. His role would also explain why he was put in 3x23 to look for what would happen with Jane. It would be the reason why he took the phone so quickly when he became aware of the trap set by Jane.

- Smith can't be Red John for the reason explained before.

- Haffner can't be Red John since he can't be the leader of the organization. He's been given instructions from Vizualize OR from Red John (since he could have lied to Lisbon).
I think he was the one that was asked to come to the hospital to make sure Sophia Miller didn't have any informations on Ray Joth there.
Haffner is definitly someone that has missions to do, those missions being given by the leader.
He may also be the one who had the role to go and see Sophia Miller ! And, why not, putting her had in the oven like Red John asked him to do. But that makes unsure two more things :
- Is Red John really the one with acrophobia, or is it Haffner himself ? If Haffner was the one who met Sophia, then the acrophobia clue isn't true anymore.
- That would explain why we can't eliminate people like Stiles (age) or McAllister (no acrophobia + age). BUT that would help in eliminating easily people like Haffner.
=> Haffner isn't Red John himself, just a minion (the one of them having a crush on Teresa, maybe asking for Red John to not kill her).

Here are the people we discarded : Partridge (dead) - Kirkland (dead) - Smith (has a role given by the leader) - Bertram (has a role given by the leader) - Haffner (has a role given by the leader).

We are left with two people : Stiles and McAllister.
I believe we won't know for sure who is our guy till 6x06 (when we will know what Vizualize is for Red John).

This reasoning makes sense, being supported by the clues given from the production out of the series (again, if I remember correctly) :
- Ashley Gable, after season 3 final : "Red John has been visible in prior episodes. You have to search for him like Waldo."
- Bruno Heller : "We can trust the list."
- Tom Szentgyorgyi : "Red John is one of those suspects [...] This is a fight between to men." => Definitly not speaking about an organization, just a man.
It really leaves is with McAllister, Bertram and Stiles (moreover, Bertram is not like a waldo actually, but well ...). Again, it goes the same way as my reasoning.

Just a thing, going for the "absurd reasoning". Starting from the statement "What if Red John were ..." :

If Red John were McAllister :
- Good sense of smell ; Walks like hunter, without making any noise (helps to introduce in people house) ; pretty smart ; doesn't hesitate to kill and laugh about it.

+ 6x03, when we see McAllister (standing) so much superior to Jane (grabbing to something on the roof, with fear) : he really likes to be superior, to have the upper hand and making Jane needing his help.

+ He is smart enough to trap normal people.

If Red John were Stiles :
- Like a mentalist, can read in mind and other things ; very smart ; knows if everything about Red John AND about Jane (where was Kristina ; what did Red John earlier and how he feels about Jane even before RJ himself saying it to Jane ; the plan of Jane to kill Panzer with the help of RJ ; what happened to Rosalind Harker because of Jane ; ...)
=> He knows way too much about Red John. The leader wouldn't let anyone divulgue so much informations to his most valued enemy. Red John killed people for less than that. Either he is scared of Stiles (making Stiles the leader of the organization, then the one that we want to be dead), or he is Stiles, or he needs Stiles by his side.

+ Stiles did very well in making Jane believe that he wouldn't kill anyone. We couldn't expect less from RJ himself, that is brilliant. He is also amused by the situation, making Jane believe from time to time that he is Red John but just gives enough clues to make it unsure.
If I remember correctly (didn' review those episodes but those are sentences that one can't forget) :
4x16, Coming to the CBI with bodyguards : "I don't want you to mistake me for Red John and shoot me."
3x03 : "I know so much more about Red John than you and him think."
3x03 : "Red John seems to be such an unpleasant fellow. If I knew even a small clue to make you closer to him ... I would cross death for you." => Hilarant, Bret. Please.
4x16, talking about Jane's demons : "They're still chasing you, aren't they ?"
I will quote Jane : "Red John has a strong sense of theater." He likes it ? That is really similar to what Stiles does with Jane, amusing himself by inventing a role and giving weird clues that can't be taken into account but would be smartly placed at the end.

+ In 4x16 : He talks about red smoke to Grace ; he tries to enroll her and likes to be kissed by this good-looking girl ; he manages to let his follower say just the things he wanted, like if he controlled his mind just by looking at him in the eyes.

+ The 5x13 "The Red Barn" : it could explain many things if Stiles was the leader and forced his minions to go and kill some people in the barn, like a training for the real missions. Vizualize members could be gold choices for future murderers : Stiles is their savior, they trust him more than nobody else.
In 5x13, the sentence "What does anything mean", said indirectly by Talbot => Wouldn't that be a way to say that he can't understand why Stiles is the demon that they all believed to be their gourou ? He must have asked himself : "Why did I follow him ? Was it really to die for him, just like that, because he decided my life ended there ?"

+ 3x03 => How convenient it is for Red J... I mean, Stiles, that the murderer (who was someone that knew some secrets of him) was killed by the lover of the victim ! Now no-one can extract information from this dead body, and Stiles isn't suspected at all. Did he control his mind as well ? Even Craig O'laughlin is there to make sure the operation is well done.

Speaking about Craig : wouldn't it be more logical if he didn't work for the FBI, investigating on Stiles (after all, FBI ALREADY has a mole in Vizualize) but was sent there intentionally BY Stiles to keep an eye on the team ? We know he works for Red John, what if it was the real deal ?

+ Red John must have had experienced a while before, maybe not only 25 years back at the barn. It must take some reflexion, backwarded by feelings that developped with age. A 15 - 20 years old guy would be like that.
That woud even surprise me that someone younger than Jane would be smarter AND with a stronger power and organization than Jane.

I definitly bet my money on Stiles, even if I can't totally rule out McAllister for now (still weird that RJ would show with two of his minions in 6x02, but well ...).
He has the power, charism, smartness, boldness, experience and organization to be Red John.

PS : Just one last thing that will help Jane in killing Red John : Jane is willing to do anything to kill him, even if it means he has to die for it to happen, while Red John struggles to survive. RJ fears death, this is not the case of Jane. That will make the difference at the end. Go for it, Jane.

I dont believe that red john is ray haffner. In the episode where teresa lisbon refuses to join haffner's private firm, haffner asks her if it is because of Jane. Haffner tells lisbon that when jane finishes catching red john, Jane is going to leave the firm. Haffner gives this as incentive for lisbon to join his company. Now why would haffner say this if he were red JOHN?

Also R E D J O H N has 7 letters. Jane also compiles a list of 7 names (just an interesting thought =) )Honestly I dont think that red john is any of the 7 guys..

One thing I really found interesting was that in Red-Listed (Season 6 Episode 4) Kirkland said that his twin brother, Michael, had serious drinking problems like his father and Red John approached him about them. Well, Visualize specializes in drinking problems so it would make sense if it was Stiles. Also, the reason Kirkland didn't see him is because I remember in the episode that introduced Visualize that a visualize member had to break off all connections with his family so he can find his true identity. Personally, I don't think it is Stiles but I wanted to make this point.

I think that , obviously Red John is a much older guy as he has been killing for years, however, the writers of the show want to create an organisation so that after we know who Red John is the show still has a storyline to continue into another season. 

If there are several people working for Red John it makes sense to flush them out in almost every other episode. What would be interesting is to see how he actually indoctrinates them into doing whatever he wants and then killing themselves when caught. 

In short i think its Bret Stiles he has that power to convince, however i don't think he has the physical capability to do so , so his killings are performed by someone younger, he is just the man behind the curtain. 

After the revelations of the last episode, we know there's a secret organization within the police forces that protect itself.

This makes me believe all the suspects of PJ's list who work or worked for a police organization is involved in this secret organization, that includes Bertram, Sheriff McAllister, Smith, Haffner and maybe Partrige too.

I believe RJ is not the head of that organization, although he knows it and knows enough about it to make it go bust. He just exchanges his silence in exchange of protection for his own crimes.

Stiles is the only suspect on the list who does not work for the police, he had many problems with justice publicly revealed but there never was any official proof. I believe this is because he was protected by the criminal organization which covered more than the public list of crimes he was accused of, like killing  detractors of Visualize, or their relatives like in PJ's case.