I wrote this in a comment earlier today, but it deserves it's own post:

Many theorists are failing to take into account something of
staggering importance. No actor has known that they are (or will be) Red
John until the very final episode of RJ with the reveal, which was
recently filmed. THEREFORE, every single voice recording we have of RJ,
and every single sneak-peak of RJ (be it in a mask, or holding a cup of
tea, or in the shadows) has been using an EXTRA actor (or a voice actor)
with no intention of them being RJ ultimately -- just to film a
specific scene for purposes of the show. THEREFORE --- we can not, ever,
take into account what a voice sound likes, what a hand looks like,
what a body shape seems to be, what a shadow looks like etc... from
previous episodes. It is completely false information. The show (Heller)
has been abundantly clear about this in interviews etc. So, please
disregard all evidence of voice samples and the like. They mean nothing.

partridge is dead because we saw his body. kirkland is dead. haffner and stiles are dead also. even if they survived they didnt have 3 dots. reede smith turned himself in and he cant be red john. 

i think mcallister got shot by jane and survived but jane thinks he is dead. i think mcallister is red john because they want to suprise the audience and in the promo we can see someone that got shot runs which i believe he is mcallister. if mcallister is not red john then bertham is red john. there are no other possibilities because they said red john is someone from the list.

Patrick waits in the church for Red John
Red John arrives and walks in the church.
Patrick: McAllister?
McAllister: Yes it is me
Patrick: Uhh you're not Red John... Your voice is lower than I've expected.
McAllister: Ohh shittt wait.. *inhales helium*
McAllister: Hello Patrick.
Patrick: OMG it's you! You're Red John!
McAllister: After six seasons I want a rematch to our first game of Rock paper scissors..
Patrick: Rock
McAllister: Paper
McAllister: "The game's over and I won."
i would laugh my ass off if Bruno Heller does this xD

I believe it is either of the prime "dead" suspects, McAllister or Partridge. Jane naming Bertram as RJ serves two purposes: putting a crimp int to the activities of the Blake Association (as Bertram is the head or a high ranking member) and drawing out RJ, who will not be happy to have someone else take credit for his achievements. Having RJ be one of the dead suspects also allows Jane to kill them with impunity. Since Cho says McAllister is confirmed dead, and Partridge is dead, Jane cannot be charged with murder for killing a dead man.

Just a few observations about McAllister.

Noticed in "Wedding in Red" how there were moments when his voice would go a little high pitched (e.g., when he said "corpse" and "hunt").  Remember Patrick said he had a speech impediment of which he was ashamed.  Whoever RJ is changes their voice when in public, but you will hear hints of "THE RJ voice" in McAllister if you listen.

Did find it interesting that when he entered the church he asked, "what's cooking" (Sophie Miller had been murdered in the previous episode).  Others have noted his keen sense of smell (like RJ in 'Strawberries and Cream').  There's always some mention of "game" --- and then in the upcoming episode RJ will declare, "Game's Over and I Won!"  I don't think for one minute that he really lost "rock, paper, scissors" --- it took just as much smarts to get it "wrong" each time with PJ.

I mentioned this a while back, but in "Wedding in Red" there are birds chirping in the church when McAllister didn't want to go up the ladder and also when he didn't look at the Bella Vista.  In a recent article teasing about the upcoming episode, we're told that we should have paid attention to the clues.  And we all agree by now that pigeons have been of utmost importance, exactly how, not sure.  As most of us noted yesterday, there is a live pigeon on the Mary statue in the church.  Are they triggers for RJ?  Bad memories?  Does "A Brace of Partridge" factor in?  (BTW: anyone have the "interpretation" for what the painting means?)

I still feel like RJ met PJ in his younger years.  We'll soon find out!

Just wanted to point out that no one seems to talking about the car that sped away from Jane's house right after the explosion.  There was a car speeding away that almost wrecked into Lisbon.  Whoever is driving that car has got to be red john.  I personally believe it has to be Sheriff McAllister since he was right beside Bertram and Smith( the only two that survived the blast).    I can also see it being Partridge.  the first thing partridge says in season 1 episode 1 is "red john enters here".
Also Sheriff McAllister shows up in the second episode so they are my two guesses.

So I would like to propose an idea entitled The Severed Foot Theory

As Lisbon enters Jane's demolished house, she waves her flashlight around and comes upon a severed foot.  I postulate the foot was NOT blown off by the explosion, but rather a shotgun blast... the same shotgun blast we hear prior to the bomb.  

Here's what happened.  One of the suspects grabs the shotgun out of Jane's hands.  He's aiming it at Jane, who panics saying, "No! WAIT!"

And then the strangest thing happens.  The suspect shoots off his own foot!  Jane is perplexed for a moment, and then the bomb explodes.  Due to head trauma, he forgets that last split second.

So why was the foot blown off?  Because the suspect wanted the forensics team to find it.  That way they would believe him to be dead.  This would also imply the suspect knew about the bomb, and therefore would probably be Red John!  

My theory eliminates Bertram and Smith because they have both of their feet.  So it has to be one of the supposed dead suspects: McAllister, Haffner or Stiles. 

From what Reede Smith tells us, someone within the Blake Association wanted Bosco's secretary dead.  Therefore, I put my money on McAllister, since he's got the tattoo.