Honestly, if a bird came out of nowhere and scared the shit out of you, you would very much act like that, i would for sure but does that mean i have a bird phobia? No. Don't over think it, honestly. 

-He first appears in Episode 1 of season 1. 
-He gives Jane odd glances and dirty looks in ep1, almost like he's mocking Jane with his eyes.
-He asks Jane if he's 'psychic or something' even though Jane never said anything about him being psychic (again, he's mocking him, because it was Jane pretending to be psychic that made RJ kill Jane's family).
-He appears out of nowhere for an undetermined reason and surprised Van Pelt.  He comes out of the woods, which are filled with PINE TREES.  In Rosalind's description of "Roy", she says he smelled of "pine, nails, and earth".
-There's a scene where he walks toward the camera in the middle of the episode and he walks exactly the way Red John does in "Red Sky in the Morning".  You have to see it.  It's pretty apparent and jumped out at me almost immediately.
-He knows how to shoot a gun, as does RJ in Red Sky in the Morning.


-He has a ring on his left hand, just like Roy had during Rosalind's Phone Call, where Roy visited Rosalind and held the tea cup.
-For some reason it is suggested that RJ is tied to police officers.  There is a policeman in the colors that McAllister wears speeding by in "The Crimson Hat".
-Also the title of the Episode:  The Crimson Hat.  McAllister is the only one who wears a hat regularly.
-The man who poisoned Rebecca was wearing a police uniform similar to that of McAllister.
-Todd Johnson was killing cops, for some reason.
-McAllister wears pointed shoes, and so does Red John.
-It is implied that Red John has a real phobia.  It is either fear of heights, or something else.  There are many depictions of birds, especially in seasons 6, implying that RJ's secret fear could be birds.  McAllister is either afraid of, or just hates birds.

-It has been revealed that McAllister is a hunter and moves with some amount of stealth. 
-He's also quite strong to lift Patrick up off the side of the roof.  RJ lifted Jane (by the chair) at the end of Red Sky in the Morning, and also saved his life, just like McAllister saved Jane's life here.

**Probably the biggest factor pointing towards RJ being McAllister is the 'handshake'.  I always wondered why the 7 suspects didn't ALL have on-screen handshakes, considering Jane shook hands with far more than seven people, and most of those people were just as obscure as McAllister.  So why did McAllister make the list even though he had an off-screen handshake?

Gale Bertram, Ray Haffner, Bob Kirkland, all had on-screen handshakes.  So if RJ was one of them, then why didn't the other suspects also have on-screen handshakes?  It would have made things so much easier.  My guess is because Bruno Heller came up with the handshake idea WAY after he already decided on who Red John was going to be, and he never filmed a handshake between Jane and that person.  The people on Jane's list who had an off-screen handshake were: Brett Partridge, Bret Stiles, Reede Smith, and Sheriff Thomas McAllister.  Partridge is dead, so he's out. Stiles is too old, if the description of Jay Roth being 'middle aged' is to be believed.  Reede Smith came into the picture AFTER Bruno Heller said that Red John had already been cast and we may have already seen him.  The only off-screen handshake that works is the Sheriff's.  And there was no reason to include off-screen handshakes unless the REAL red John never shook Jane's hand on-screen.

Also, one last thing...out of all of the final 7 suspects, which one seems the MOST out of place?  Think about it.  Everyone other than Stiles and McAllister is part of the CBI/FBI group.  McAllister and Reede are the only 2 who were seen just once before season 6.  McAllister is the only one who was brought back ALLLL the way from season 1, and who was NEVER in any other episodes (that we know about).  Stiles was in several episodes.  McAllister's slot as one of the 7 makes absolutely no sense on any level.  If he was meant to be a bluff, there are much better, more believable bluffs (Royston Daniels, Ellis Mars, even CBI Ron).  He's the least-likely suspect because of our lack of knowledge about him, and the fact that we haven't seen him directly for 5 years.  So why bring him back, unless he isn't a bluff at all?

The way I see it, there's a kind of symmetry within the show itself if McAllister ends up being Red John.  The person Jane meets at the very start was all-along his greatest enemy.  His journey could have ended as soon as it began, but he didn't see it, because he wasn't looking for it.  We the viewers also weren't looking for it when we saw it.  So in a way, we went on Jane's journey with him, and everything has come full circle.

Sheriff McAllister: What? Are you clairovoyant or some gizmo? You got psychic powers? Patrick Jane: No. No powers. Had 'em once. I mean I pretended I had 'em obviously. No such thing as psychic powers. 4x24 http://www.youtube.com/watch?v=pDqVYNtTso4  min 3:33 sheriff car ?  police car on a covert operation fbi-cbi ??

again we see what happened in the episode 1x02 rigsby helps the sheriffanother thing is way too nice to the CBI"Tom" tells you everything you need game face (because it's so suggest the sheriff)In the dome says  "the way in which got into the case as if tubiera a hidden agenda" again talking between the lines

sorry my english i from sudamerica

GUYS, THIS IS NOT ROCKETSCIENCE. EVERYONE KEEPS ASKING WHAT DOES HE IS MAR MEAN? FOR THE FINAL TIME HERE IT IS; HE IS MAR = SHERIFF THOMAS McALISTER                          HE  I                   S M  A         R

My bet is Thomas Macallister; he is a sheriff, he moves in the country, he has a lot of freedom to do what he wants. He has no living family.  His blood lust can be easily seen: as well as his primitive strength necessary to be red john. What it is not evident its his intelligence (but as Jane recognizes, he looks more dumb than what really is).  He is an old fox knows how to move without being seen (see Van Pelt season 1 episode 2), he needs to be in total control of the environment around him in order to reveal himself(he admires Bach rigor in music). Brett Stiles knows him as it should be since they have similar ages(probably they were kind of buddies at the Ellison farm).

This is not really a good theory about who is Red John, It's more about the relationship between Kirkland, Bertram, Reede Smith, McAllister and Darcy.
I think that they all think Jane is Red John (for some good reason, I hope), remember, Darcy says something about it in 4 season.
Kirkland is watching Jane since he became a CBI consultant. So, Kirkland called this "time" to keep an eye on Patrick.

But we all know that Jane is not Red John.

I think Red John is Thomas McAllister. He is taken out from suspects by not having fear of heights at the end of the episode, but he is afraid of pigeons. In S06E02 we learned some things about Red John, including that he may have a fear of heights and can whistles really good, all those things have been explored, but not the pigeons. They appear in the first episode of this season and has not yet been cited by Jane or anyone besides. Still in S06E02  the camera focuses in the hands of this strange lady who is feeding the birds. 
I believe that Sheriff Thomas McAllister is cheating with Kirkland and all others. 

I also believe that there is an important role for Bret Stiles, there must be a reason why he has been included in the list of suspects: Shortly before the list episode , we learned that Red John is a middle-aged man, who had less than 30 in 1988, in addition, Stiles does not match the Rosalind description.

I am Brazilian, and I don't speak english, so i don't know if I made myself clear. If you can't understand something, please comment and i try to write better. And I'm sorry if someone posted some theory like mine before, i never see one similar. 

Hello
i noticed something may be a clue or not we will see
i noticed that when mcAllister give a hand to help jane in the s06e03 last scene he use his left hand ( sure )
and in season 4 episode 13 when roy with Rosalind Harker he use his right hand to hold the cup of coffe and when he sits down he grab the cup by his left hand to drink the coffe
but >> something make me have no answer in season 2 last episode when RJ kill the girl he uses his right hand ??? How i do not undrestand this >> if RJ and ROy is the same person how they uses different hands ?????!!!!!!!
thanks