First I want to say something completely irrelevant to my theory, I had a dream where it was in fact CBI Ron who is Red John. I think I've been watching the mentalist too much lately and I do think about who could possibly be Red John every single day since the end of season 5..


I'm going go through some of the major points why I believe Thomas McAllister is Red John, Some of the points I make are not originally mine.

The scene with Van Pelt in the forest and McAllister acting like a serial killer with his next victim is one of the very first clues that point to him being Red John

The handshake clue given to us by Lorelei Martins was referencing the rock paper scissors game between Patrick and McAllister. If Red John told Lorelei that he shook hands with Jane it's unlikely he would've went into details saying it was a metaphor for the game they played.

He's been with us from the beginning, originally my red John suspects where pretty much Partridge, Minelli, Wagner and McAllister in no particular order at that point. Throughout the first season there where numerous references to sheriffs and marshals which all could be clues pointing to McAllister.

Being the Sheriff of Napa County coupled with the fact of being part of the Blake Association would give him the mobility to be Red John.

The 10 years of no murder could have been while McAllister was working his way up in law enforcement in Napa County and possibly working his way up in the Blake Association.

There have been multiple references of wine throughout the show which could be cluse pointing us towards Napa Valley

The age thing has always bothered me from the start, McAllister being younger than the actor who portrays him. 

Red John has a fear of Pigeons, Lisbon opening the door in the house where Partridge was killed allowed them to escape thus interrupting Red John before he could finish the job. Later it was shown that McAllister could have a fear of Pigeons.

He is Mar, the M is for McAllister, the a could be a smudged/blood drip forming a dying man's C, and the r could be the start of an a. The one flaw here is why right he is? Seems like a waste if your dying I know. Can't explain that. 

Red John may be ambidextrous and it is possible to deduce that McAllister is also ambidextrous with his hand placements, the way he holds things/walks etc.

He fits the Red John description,of short straight hair and his height fits.

I believe McAllister is the only one to have actually saved Patrick's life. The fear of heights was a red herring earlier on in that episode which we ruled out when Patrick was saved on the rooftop causing us to not read too much into the fear of pigeons explanation. Also McAllister is one of the few suspects to get along with Patrick.

McAllister was first presented as a dumb, small town sheriff but is later shown to be able to match wits with Patrick when they solve a murder case together. There is also a strong playful chemistry between both Patrick and McAllister.

The bomb in the hat theory works for the explosion, McAllister was standing far enough to not have been killed in the explosion, and DNA was placed with the bomb to fake his death. 

And my final point is that Red John likes the use of first names which is what friends do which is why McAllister asks Patrick to call him Tom.


Mostly circumstantial evidence, but that is mainly what we've been given about Red John. 

Not a theory, just wanna share my thoughts:

Honestly after last episode and seeing ep. 8 promo I no longer have a clue who may turn out as Red John, and that kinda makes me sad because until now i was convinced it's going to be Partridge and after what had been shown to us in ep. 7 when Cho "examed" Brett's dead body it would just be too obvious for him to be Red John. Of course Brett a.k.a Red John fans (no offence, I'm among you guys:D) might say that we actually never saw his face, but unfortunately I'm now pretty sure he is really dead. Why? Ok let's start.

Bruno Heller did cheat all of us saying that in the end of first episode he left us a big clue. He really did but it is rather a clue that really became one after this episode when Jane was interrogating that police officer.

PJ: There's a password, too, something you say|as a greeting or a... Distress signal. "Tiger, tiger".

That actually turned out to be that clue. As we now found out the Blake Association is big enough that members don't know each other - they work in groups, and don't know how about you guys but imo, the Blake Association isn't proud of Red John being a member (Smith reacts in a way as he is unhappy because of it). Conclusion: Brett Partridge actually wanted to warn Lisbon and tell her to gtfo of that house but he knew if he just say that Red John is going to kill her so he used "tiger tiger" in hope she is a member, too. Unfortunately he didn't know Red John is a member and didn't expect that he would react.

Why do I think that was the clue?

Because after interview with Heller we all started to look for a possible clue. Some of us tried that stupid 666 theory, some of us hit "pigeons theory" but for me all of this turned out to be Red Herrings so we could spend our time thinking what did we miss.

What does it mean in recent events?

Brett Partridge - dead
Bob Kirkland - dead
Reede Smith - in jail (probably if he's going to survive)
Bret Stiles - no tatoo, simply too old to be RJ
Raymond Haffner - Jane doesn't care about him, he speaks free about RJ near him and he insults Ray, i think Jane wouldn't be stupid enough to provoke RJ again as he know how it end up first time.
Gale Bertram - on the run, just a ordinary member of Blake Association.
Thomas McAllister - it might be him (i think it's the guy running on the promo) but it would be a huuuuuge mistake to reveal RJ identity in just a Promo lol, who does that? We've been waiting for this moment few years....

Conclusion

1. Red John is not on the list and all that we witnessed from episode 5x22 is Jane's deception.
That actually would be a perfect solution because each episode is focused at another "suspect" and each week we all change our theories/thoughts about who might be Red John and we miss the most possible option.
If Red John is someone not from the list i think Walter Mashburn woul be just perfect.


2. Kill me but - Brett Partridge, but honestly im not going to point out why because we all know why.

Just a observation

Did you notice that guy moving Jane's couch, he gave him his coins but he had "FBI" at his suit so how on earth FBI guy would know Jane used to spent 90% of his time at that couch.

Red John must had been present in team Lisbon room and we must have seen that.
And that makes Walter Mashburn 1:0 Brett Partridge.

Cheers

CBI Ron IS Michael Kirkland - just with a beard and a little extra weight.  He has been quietly manipulating PJ from the sidelines this whole time.  He IS Red John.

Gale Bertram simply would not have the time or the privacy, as head of an agency such as this, to have the geographical range to do all the things that Red John has done.

Reede Smith is not bright enough.  Besides, he hired on with the FBI too late - their background check would have caught SOMETHING suspicious.

Bret Stiles actually DID become friends with PJ after they shook hands, so Lorelie's statement would make no sense if it were Bret Stiles.

Sherriff Tom McAllister has the same issues that Gale Bertram would - not enough time, privacy, and geographic range as the sherriff of an entire country to do all that Red John has done.

Ray Haffner isn't smart enough and doesn't have the personal charisma necessary to get ANYONE to do something he wanted them to do.

Bob Kirkland is dead.

Brett Partridge is dead.

As we have all seen throughout this series, Red John moves his pieces around the chessboard from the sidelines, rarely, if ever, actually getting his own hands dirty with something as menial as actually covering up his identity.  This is his way of living the life so desired by someone relegated to performing menial tasks on a day to day basis.  This is the essence of what drives Red John - and THAT is CBI Ron personified.