I am happy that Thomas McAllister is highly likely Red John, my most favourite since season 1 episode two.
Look at this when PJ asks Thomas to stand up, he smiles. Just like he has planned something, the bomb.
http://thementalist.wikia.com/wiki/File:McAllister_smiles.png

Thomas stands with the most distance of the bomb, because he knows. Look his posture and his legs, as if he is about to escape.
http://thementalist.wikia.com/wiki/File:McAllister_away_from_the_bomb.png

Red John walks in the church with a gun on his right hand.
http://static3.wikia.nocookie.net/__cb20131120035016/thementalist/images/6/65/RJ_vs_Jane.jpg

The reason why Red John got somehow distracted and got shot by Jane. Phobia.
http://static3.wikia.nocookie.net/__cb20131120040545/thementalist/images/5/57/Pidgeon_6x08.jpg

He got shot, and his stunt man said a month ago that he was a stuntman of Thomas.
http://static2.wikia.nocookie.net/__cb20131120035226/thementalist/images/8/8c/Possible_RJ_escape.jpg

Red John's hands
http://static2.wikia.nocookie.net/__cb20131118225815/thementalist/images/e/ed/Unkzs.jpg

I'm happy that he is Red John.

All credits to:
http://thementalist.wikia.com/wiki/User_blog:Manuel_de_la_Fuente/And_this_is_Red_John...

I'm actually quite happy that I got it right even before epsode 7 and the promo.

Here are some of my previous theories:
My most funny one
http://www.whoisredjohn.com/See-a-theory-Red-John/12706
My most accurate one
http://www.whoisredjohn.com/See-a-theory-Red-John/11543
And the one with the most characteristics.
http://www.whoisredjohn.com/See-a-theory-Red-John/12575

If the photo links aren't showing correctly I will correct the problem to post it in the comment section.

And hey friends it's cool that we all love The Mentalist, let's all enjoy the final episode of Red John. We should be happy and enjoy the theories instead of bickering!

Sincerely,

ThePhantom/PhoenixWright