Red John is Ray Haffner.

Lorelei Martins said her sister's death set her free and brought her to her full reality. Do you really think she would hear deep thoughts like this from silly Smith or Bertram or the sheriff? The only people who can teach her these kind of things are Stiles and Haffner. She was an intelligent, beautiful woman, she would not have been attracted to anyone else but Haffner or Kirkland maybe. (the same goes for Rosalind and Kristina Fry - just imagine them with Haffner, nobody else comes close)

And there is the voice. We know Red John speaks in a gentle, soft voice, more people confirmed it. Do you really think when Red John spent months with Rosalind, he had a 'thingy' with him everytime he talked to her? (don't know what the thing is called that changes the voice). Haffner has a soft voice, so did Kirkland but none of the others do.

And then there's Sophie. She seemed to think he was an interesting, pleasant person who is hiding something. Just imagine Haffner talking to her; he is the kind of person who would hold back a lot of things while still being pleasant and nice.

Sometimes there's no need for complicated theories because everything's simple.
He has short straight hair, he is not thin and not too muscly, he is the right height, he and Patrick or not friends, etc..

Haffner is Red John.