I am certain, more than ever, that it's Sheriff McAllister. The clues are right there for the taking. Adding on my theory here that it's McAllister: http://www.whoisredjohn.com/See-a-theory-Red-John/10471, here's why I'm ever so convinced after watching 6x07.

1. RJ is smart, he would've faked his own death in the bomb. He didn't bring the bomb to get rid of the other suspects, he brought the bomb in to write himself off the list. We all know RJ by now, he isn't stupid enough to get identified. We know RJ is part of the Blake Association. McAllister plants blood samples knowing it'll match positive to him and the team will pronounce him dead. NO ONE WILL LOOK FOR A DEAD MAN. And thus, ladies and gentlemen, RJ has successfully written himself off Jane's list. Whether Jane made it out alive or not, no one would still know of his identity. And now, while Jane blindly hunts for Bertram, McAllister is free as a bird to screw around with Jane one last time. Absolute Red John genius there. 

2. Bertram uses an alias in the vault - and it's Thomas. You can't get any more obvious a clue than that. BH and the writers are just throwing it in your face by now. 

3. The 6x08 promo. That man is not Bertram. It's Xander Berkeley aka Thomas McAllister. Go watch it for yourself.

4. The pigeon. It's in the promo. It's a symbol. A clue. The pigeon that Lisbon released scared off McAllister. He made it clear on the church rooftop that he hates pigeons. And now we see one in the promo. 

BH keeps to his word that RJ has been there from the start. RJ as Bertram is a disappointment. Yes, Bertram, as the head of Blake Association, makes all the sense in the world. But him, as RJ, does not cut it. There are still so much more lose ends to tie up before next week (the coded list, the dodgy FBI agent from Texas, why Partridge's left shoulder got skinned). We all know and love this show and there's always, always more than just what's been thrown at you.