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.

I've rewatched the episode 3 times now, ignoring the obvious clues/red herrings (fear of birds, middle aged, good posture, able to creep silently), and that one moment on top of the church, just before he extends his arm to PJ says a lot to me. In a body language sense, i read that he feels totally in control, almost as if he's sending a message to PJ, saying "I don't have to rescue you, i can kill you at any moment, but why spoil our game?"

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