Red John is definitely Thomas McAllister. Now I will explain why.

1 - The actor who plays TM, Xander Berkeley (http://www.imdb.com/name/nm0075359/) has done voice work in his career, this means that he will be able to perform the weird Red John voice we have heard throughout.
2 - He is scared of pigeons/birds, this is why he had to leave Lisbon, the pigeons were scaring him, this is the fear the he was hiding from the psychologist (he claimed to be afraid of heights due to it being way more generic, so less identifiable). Pigeons have been hinted at all the way through the season in the promo for the next episode there is a pigeon sitting in the hand of a statue in the church.
3 - He is easily old enough to be at the barn and be RJ.
4 - Download the 'Red John - S06E08' trailer and play it frame by frame, look at when RJ crashes through the window. This is McAllister, there is no doubt about it. The hairline is exactly the same.
5 - Also I have rewatched some of the RJ episodes and paying loads of attention and if you look when RJ saves Jane (S02E23), he is wearing heeled boots. Who else wears heeled boots but sheriffs? Although this may be insignificant as I doubt it was thought about that much.
6 - Faking a death in an explosion is easy as pie. McAllister is pretty old so has probably got fake teeth so the one identifier on charred bodies is not working (ok, this is a bit of a stretch). We were given no real confirmation they were really dead, we saw one foot that's it.

I must also say why I don't believe it was others.

Bertram - Too obvious, next episode was always going to be the big reveal, Jane only released his name so he could take attention off of him to work alone. Why would he give up his vengeance so some randomer can kill/capture RJ?

Reede Smith - If this needs to be explained to you, how about you go and actually watch the show.

Brett Partridge - Dead. Tattoo cut off for security reasons. Guy was an absolute weirdo so got in TygerX2 because he needed someone to cover up for him doing some WEIRD stuff.

Kirkland - Really dead. Don't think it's him. Twin must have some significance? Or just something to put us off.

Bret Stiles - Too old, British accent is identifying although could be hidden. Not much against him but I've not got much the other way either, so he stays a second option.

Ray Haffner - He just doesn't fit. Seems as though he was brought in to fill up the list really. My main point against him is that he holds little power, the rest, bar Smith, do.

I probably left out loads of things I should have written, but anyway, now you know who RJ is. Thank me later.