-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.