Ok, so, firstly, for all of those people that think Red John is Bertram:

- it  would make sense, but it is definitely too obvious for it to be him because the mentalist is known for it's plot twists.

- and if it was Bertram, then at the end of season 3 (Strawberries & cream) then the assassin sent to kill hightower would have gone to the room that they told bertram she was staying to find the CBI Red John accomplice that burnt Todd Johnson alive (granted, she did go to that room but it was only so she could climb to the other room with the rope). as Bertram is part of the Blake association, then the assasin could've been ordered to check both rooms for Hightower, this one was just a mixed up thought that i haven't described well haha.

but i think bertram is more than just a tool for red john, he is closer to him.

so, i think that if red john is anyone on the list, then sheriff mcallister is red john because:

Firstly, He is alive, and one of the bodies found after the explosion wasn't him. Say he is red john, then he wouldn't bring a bomb into Jane's house without a backup plan. He is cleverer than that. So he makes the world think that he is dead in order to draw away the suspicion that he is red john. Also, an interview i read somewhere, went something like this:

Interveiwer: so are we sure that those three died in the fire? and it wasn't a trick/plot twist?

Writer: well, yes, is was real bodies in that house, but there are some surprising turns coming up regarding the explosion.

notice how he dodged the question and gave it away a bit?

-in last nights episode (The Great Red  Dragon) Bertram went to a vault storage room thingy by the name of Thomas (which i think is Sheriff Thomas Mcallister) and my theory was confirmed when there was wine bottles in there, because Napa is the wine country!

So you may be thinking 'say that is McAllisters Storage room, that doesn't mean he's Red John' 

well, there are several reasons why this could mean that he is Red John. Firstly, he could've contacted Bertram and asked for a favour (which he had to do as part of the blake association) to go into his storage and get passport, money etc. and plant the fake lighter USB stick with a code message, knowing that jane would solve it (i suspect it told him to meet him in the church because jane doesn't believe in God so why would he go to a church, and he wouldnt just let go of the RJ investigation like that after 10 years of devoting his life to it, so just told Lisbon he was giving up for the same reason he left her by the sunset and drove off in 'Fire and Brimestone')

And also, if you look really closely, after Bertram opens the box in the storage room, when he lifts out the straw-like packaging first, i think you can see that buried in the straw packaging, there is RJ's signature knife (the weird shaped one RJ is seen holding in many scenes).

so yeah I guess thats why I think it's Thomas McAllister

Also, does anyone have a theory for why there are pigeons emphasised in loads of scenes (the scene in the house where partridge was found dead, in the promo for 6x08 on the angel made of stone in the church and various other scenes)

This is probably all wrong but thank you for reading and feel free to comment! :)