-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

After watching episode 6x03 I don't think we have more reasons to suspect McAllister than we did before. What did or said doesn't prove anything. we can say he's RJ because we can see everything we know (or we are made to beleave we know) about RJ to discribe this guy!
Well no. We have not made any progress if everything he does or say can be also explained in a logical way. Why. Because then it's up to Heller to deside if he is RJ and make it happen.
Only things that could not be explained in other way than him being RJ, can be taken into account. Why? Because we have strange things for every other person in the show, that could be explained with that person being RJ.
So. What did McAllister did in this episode? CBI arrives at his jurisdiction and takes over.
The same happened in episode 1x02 and he was not happy about it, although he wasn't showing it much. Then he got emparased with Van Pelt and he didn't solve the case, Jane did.
So we expect him this time to be polite, cool, cooperative and not get in their way in a way they would get offended.
At the same time he has to show any way he can that he is sheriff for a reason and he isn't useless. And we all see that he does more than that in the end.

OK in the chapel Lisbon tells him to climb the ladder to get a hammer. Well nice is nice but he wouldn't do labor for these guys, he can get others to do work. So when he says about he would need other shoes, it's obvious that he is in the sheriff's shoes, and their errand boy. Look at the that scene. Can you see him standing like the authority he is?
Later at the cliff Jane tells him "come over here fela have a look". Well he is no "fela" he's the sheriff! Doesn't mean he's suspecious that he didn't go. And don't forget thet he was interupted.
From then on he is the nicest guy really. When Jane tells him he and his men need to hang back while Jane puts his plan to work, McAllister has no problem at all.
After he saves Jane he finaly tells him that he ignored him telling him to hang back, because he didn't trust them the way they forced their way to this case. He is still polite though. As for the pingeons flying to his face, well no one would like that.

Personaly I don't see anything suspicious about McAllister in this episode.