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.
