Just a little theory for those who think that Red John is Walter Mashburn.
If Red John is indeed affected by acrophobia then Walter Mashburn can not be Red John. Remember the episode 2x12 where the Lamborghini of Mashburn falling off a cliff. Then we can see Mashburn approaching the edge of the cliff to watch the rest of his car without apparent fear. He probably would'nt have been able to do that so easily if he was really affected by acrophobia.

Oh cmon guys Bruno Heller is a mastermind, how can you be fooled by a sentence such as Bertram's: when you catch red john i'll be there or when the psychoteraphist says that mr. ROTH is a good whistler and McAllister is shown after,... You must look at the smaller picture, I can guarantee Bruno has our eyes and minds compleatly messed up with those ''BIG CLUES'' but in the end, like said before, the birds which are shown in many different episodes ( all include RJ ) will be the main clue to RJ, or something like that.. 

So i must say that I think that no one of the seven is RJ, they are all his friends and they know about each other ( the meeting ). I also think that Bret Styles is RJ's father, and Bob Kirkland is RJ's brother. I must also say that Teresa Lisbon might not be murdored ( yet ), because she is the weak part of Jane, he would do anything for her and I think RJ will soon start to use her as a bait to mess with Jane. So I must say that I dont know who RJ is but I will say that we are missing something... Bruno Heller GREAT JOB :) <3

It's Ray Haffner! When Sophie mentions the excellent whistler they take our attention off Haffner by showing McAllister. Remember Haffner whistling at the hosital...
Middle age: This rules out Stiles and Bertram in my opinion.
In good health, showing Haffner doing his workout is a hint of this for me here. 
I think of Kirkland as Red John's right hand man. 

All the signs are pointing to Haffner for me ;)

It's gotta be ray hafner. Doc described him to a T and leaving lisbons hospital bed he whistled on his way out. At the time that stuck with me as creepy but she said he's a good whistler so that's gotta be the reason heller made him whistle. Bob Kirkland could be Rj but I thought it was ray since the end of last season. I think eventually Lisbon will remember him whistling leaving this hospital room. Either way this is gonna be a great season!

My top 2 choices have been Ray Haffner and Thomas McAllister, and last night's episode further confirmed my belief.

Several things I've noticed:

1. When Lisbon tells Haffner that RJ did not hurt her, he does not give the response you would typically expect from someone who's genuinely concerned.  Instead of saying "wow! you got lucky! That's great!," he responds matter of factly "good for you."  It almost seems like Haffner wanted Lisbon to get hurt, but somehow the plans got foiled.  Perhaps RJ has a phobia of pigeons and had to leave the house due to all the birds?

2. During the meeting with the 3 RJ suspects, Bertram and Smith look visibly nervous while McAllister is not.  He looked genuinely surprised, as if he has no idea what Jane is talking about.  Perhaps RJ is a great actor?

3. Based on Sophie Miller's description of "Jay Roth," I think we can safely rule out Bret Stiles and Reed Smith.  The former is not middle-aged, and the latter is obviously not in good health.

4. I think the big clue in the last sequence of the season premiere is that Red John is left handed.  On last night's episode, we see Sheriff McAllister walking casually.  His left hand is at his belt while his right hand is swinging freely.  Something off about that.  It's not how normal men walk around. 

5. I think there's a good chance that Haffner is Stiles' son.  I don't think Stiles is RJ, but he definitely knows who RJ is and has a connection to him that goes way beyond what anyone else has presumed.