First of all I'm not sure who red john is .I had great theories but now...

Jane's narrow down the list of seven Red John suspects
I still can't understand how jane could possibly know where everyone could be in the time of RJ's murders.( he knew where mashburn or others were ? )

Fake list . 
I read somewhere that Jane reveals that a list of fake Red John suspects he planted was stolen, and the team realizes these men are in danger, so 7 suspects are fake or what?

whistling :
Like last season's handshake. Now suddenly people in show start whistling.

show's Orientation :
In this season they trying to make bertram and haffner look like the main suspects . bertram's dialog in first episode and haffner in second !

Bad feeling :
honestly I am feeling stupid for spend so many hours to watch and analyzing clues .

I Just hope they have a strong explanation about everything .

Thanks for you time and sorry for my bad english 

Rosalind Harker description about Roy Tagliaferro:

"Just under 6 feet tall. Not muscular but not soft, either. Short
straight hair a gentle voice. Rough, strong hands. He smelled of pine
and nail and earth and he liked to listen to me play the piano."


Now, Sophie Miller description about Jay Roth:

 "He’s middle-aged, in good health, with no stated prior history of psychiatric issues...He’s well-spoken, good posture, self-possessed...
However, there is every indication that his phobia issues are real whether acrophobia or some other issue remains to be seen."

We got the biggest clue now next to the handshaking, that's a phobic!

At 6x01 episode we saw the pidgeons in the room where Lisbon opened.
Patrick told Lisbon at the hospital: "Maybe something spooked
him and he couldn't go through his usual routine." At 6x02 we saw again pidgeons when the old lady feed them. Hm, it's weird!

Is it looks like Red John has an ornithophobic? - Very possible!

I don't think RJ
fear from the 666 number, but this is the alternative possibility,
beacuse that is also kind of phobic (Hexakosioihexekontahexaphobic). We saw 666 number on the wall at 6x01.

At the 5x08 Lorelei told Jane about the
handshaking, that was really big clue!
The fact is, we saw only 3 men shaking hands with Jane from the 7 suspects before Lorelei told it: Bertram, Haffner and Kirkland.
Brett Partridge is dead. Bret
Stiles, Sheriff Thomas McAllister, Reede Smith are out of the picture,
because we didn't see shaking hands with Jane before. Sheriff, Stiles, Bertram aren't middle ages by the way and Bertram hasn't got a short, straight
hair and he taller than 6 feet (6'3''). Bertram responsibe for get information the Red John investigation
(said Smith).

So, only 2 suspects left: Robert Kirkland and Ray Haffner.

Kirkland: He is 5'9'' tall (just under 6 feet). 44 years old now. He was 19 years old in 1988 (Elliston farm where 2 men killed by Red John). Exactly fit to description.

Haffner: He is 6'1'' tall (more than 6 feet). 46 years old now. He was 21 years old in 1988 (Elliston farm where 2 men killed by Red John).

At the Red Barn episode Father Peter DiBuono told Jane the smiley painted on the barn by some kid.

I'am absolutely sure Robert Kirkland or Ray Haffner is Red John!!

Hello im folowing this site over a year and never post a theory.

my thought changes a lot about the identety of RJ as im sure as evreyone..

so...as we all see in season 6 the pidgeons seems to be in ep 1 and 2. and we know that heller said that there is a huge clue in the begining of this season.

now i look into the brace of partridge picture by whiliam blake. and also look in google "partridge" and i found this pidgeons... i belive the partridge is RJ but maybe a brother of the one we know or something like that because of his death.

think about it..why this pidgeons take place in the episode and the camera let us see them? this is the only thing i can come up with

I'm going to try coming at this theory in reverse.  Instead of looking at who Red John might be, let's see how many people RJ likely cannot be.

In analyzing this, I'm not going to rely on anything Bruno Heller has said. He isn't going to want to expose the game too early, so I don't think we can be sure when he might be literally truthful, and when he might be misleading-without-openly-lying.  Plus, as others have noted, there could be times when he basically has to lie.  For example, if Brett Partridge really isn't dead, and some interviewer asks Heller whether Partridge is really dead, Heller has to lie (or mislead).  He can't just say, "Nope, that's a misdirection."  ;)

I'm also not going to rely on anything we supposedly "know" from Rosalind's descriptions, or Sophie's observations.  Why?  Because Rosalind (by her own admission) loved him (and therefore might have tried to plant false information to protect him), and because Sophie's observations were actually made about "Jay Roth," and we're technically only speculating that Jay Roth was Red John.  It's possible that he wasn't, and that RJ killed Sophie for some other reason. (Or that he did see Sophie, but not as "Jay Roth," etc.)

So I'm suggesting these eliminations on meta- grounds or logistical grounds, not based on what some character or another said...

RJ can't be Jane, Lisbon, or Cho.  Why?  Because the show is continuing beyond the Red John story arc, and those three characters are remaining on board (with no indications that one of them will be consulting from prison or something).  Obviously, at the end of the RJ story arc, RJ will be dead or imprisoned; if he isn't, it wouldn't be the end of the story arc.

RJ can't be someone whose normal responsibilities cause his schedule and/or movements to be too closely watched or restricted.  I think this definitely eliminates Bertram and Stiles; they're too high-profile.  It probably also eliminates McAllister; being the Sheriff of Napa County would keep a man's time and whereabouts pretty well accounted for.

I think those are just about the only ones we can pretty firmly eliminate.  If we conservatively speculate a little, we can probably eliminate a couple more...

Let's accept that the killings at the Visualize farm are the work of RJ and not, for example, the inspiration for RJ (i.e., not a precursor). If they're genuine, that certainly eliminates Van Pelt, and very likely eliminates Smith and Rigsby, as being too young.

It also means we have a ten-year gap with no RJ killings, from 1988-1998.  That's unusual for a serial killer, so logically, there must be some reason for the gap.  It's probably not due to imprisonment, because that seems like it would be far too easy to check; if a likely suspect happened to have a big ol' chunk of prison time in between two RJ murders, I think someone would have figured that out by now.  ;)

Most likely, he was training for something, and getting himself into a position where he could carry out his killings safely. A law enforcement position of some kind would give him visibility into the plans of authorities that are trying to catch him. That would fit Kirkland, Haffner, or Partridge. If Partridge is really dead, that seems to bring us down to two possible suspects.

Out of the two, my money would be on Robert Kirkland...

Let's not forget what Jane taught us, Occam's Razor. The simplest solution is usually the correct one.

If first of all we assume that the list of 7 is correct, as Heller has confirmed this in his interviews. We can move on from there. We can go through the process of elimination by matching descriptions given by the Rosalind Harker, and the latest physical description provided by Sophie Miller. 

Since we are given to understand Red John (Jay Roth) is middle aged, we can eliminate Bret Styiles.

Now, looking at Red John's build we can eliminate Reede Smith, as he his too obese to match the description.

I believe we can now safely say have successfully eliminated two of the seven suspects.

Now our next assumption is going to be to believe what Lennon told us during his die moments were true. We know that Lennon has met and seen Red John in person. But when Bob Kirkland asked Lennon “Do you recognize me?” Lennon replied no. Using this we can eliminate Bob Kirkland from a suspect as Red John.

Moving on to the more difficult suspects. Gale Bertram. This is a rather shaky and circumstantial evidence to use, but bare with me. We were told Red John has short straight hair. Whereas Bertram is bald. Using this, albeit unsatisfying, we can cross Bertram off from our list.

We have reduced our suspect list from seven to three: Brett Partridge, Ray Haffner, and Sheriff Thomas McAllistar.

On to our more dangerous conjecture, we have to believe Heller’s word, and the story up till now, and assume that Brett Partridge is dead. Please understand that this is no more believable to me as it is to you, since many of us are saying he could actually be alive since Partridge’s throat was not slit. And up till now we observed and believed that Red John murders his suspects by first slitting their throats and then carve their body afterwards.  

Now our Red John suspect has been narrowed down to just two: Ray Haffner and Thomas McAllistar.

At the moment, either of these suspects could be Red John, and we have not been given enough facts or evidence to eliminate either one. At a time like this all we have is our intuition. Let’s go back to season one. Out of all seven suspects, the only suspects introduced to the audience were McAllistar, and Partridge. Partridge has always been the number one suspect in this site up until his “death”. Leaving us only McAllistar from season one. Of course, there was that creepy encounter between Van Pelt, and McAllistar. But aside from that, let’s ask ourselves why a famous actor (Xander Berkeley) was used to portray a lowly town sheriff in the very beginning of the show. I cannot think of an answer, except for Heller’s plan to reintroduce the sheriff again in season 6. This stands out slightly to me, and makes me believe McAllistar is the “more likely” candidate for Red John.

For a summary of what we have determined here. We have confidently eliminated Bret Stiles, Reede Smith, and Bob Kirkland by carefully using the evidence provided to us by Heller, and assumed it to be correct. Afterwards we removed Gale Bertram by looking at the physical description for Red John for which he did not qualify. And then we had to eliminate our most promising suspect, Brett Partridge, because we are given to believe that he is dead. Now lastly, although we could not eliminate either Haffner or McAllistar from our list. We used reasoning to determine the more likely suspect, which is Sheriff Thomas McAllistar.

Possibilities I chose to exclude:
Although it may look like there is some kind of alliance between McAllistar, Bertram, and Smith. I do not believe it to be greatly significant as of S6 Ep 2, because the bits of conversation that was provided was too circumstantial to make any speculation. The other theory which is highly regarded is Red John is more than one person because of references to the Great Red Dragon. References from other literature are really not my forte, and I chose to leave it out of the theory.

Thanks for the read, only a more episodes to go!