Having seen every episode, i cant say who red john is. For me, there is only two things which must be taking into account.

firstly it cant be the split personality of Jane himself, the episode where Jane is tied up and red john kills his would be killers, whispering "tiger tiger in his ear", rules that theory out.

Secondly, the final episode makes it quite clear that red john is in, or has been in Jane's head. he knew the list and also the memory.

I think its fair to say that the whole show is about the manipulation of the mind, is it unreasonable to think maybe Jane has in the past been hypnotised to give freely information and not remember doing so?

I love the show and pray that it doesn't run too long, with two many twist .. leaving only one option as  an ending, that of Jane in a mental hospital and the the characters being staff in said hospital. I'm of the opinion that the season 3 finally in the restaurant was the perfect ending.