I continue with my theory Sheriff Rj   Dr. said that whistling good, well Haffner whistle, but not very well... at the end is the that whistling Sheriff gives to think many things but highlights a tidbit Bertram had said that they had a private meeting Jane refers to as to Sheriff,, Sheriff mcAllister and the sheriff say Tom also answers the great confidence. The Sheriff tells details of operation in the zone . see the scene 4 times remembered an important detail of RJ that when you open the door the first thing you see is your smile and drawing Jane opened the room the first thing you see is the Sheriff

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.

I don't think that there wasn't a leader.

When Patrick tells about how his former psychatrist was murdered Reede Smith looked to Sheriff Thomas McAllister like what the hell have you've been doing, I am shocked (almost disgusted) by it. 
So I think Reede - with 3 e - ;o))) works for Red John and Call me TOM ;o) is Red John.

You guys are overthinking this.
Put yourself in Heller's shoes. As a head writer, you can't plan too far ahead. Only two suspects of the seven appear in Season 1: Partridge and McAllister. Now that Partridge is out, only McAllister remains.

I can't believe that I missed this before. If you see "Red-Hair and Silver Tape", this is kinda a really creepy conversation :

Mcallister : Who is this guy?

Lisbon : He's a consultant. You want CBI assistance, he comes as part of the package.

Mcallister : (@ Jane) Consultant, eh? What are you, clairvoyant or some gizmo? You've got psychic powers?

Why did he come up with the 'consultant' thing in the first place? Also, when you see the look on Mcallister's face, he's not mocking Jane. He's taunting him..

Yep, he is whistling much better than Haffyboy ;oPPPPPPPPPPPPPPPPPPPPPPPPPp

Now we all know RED JOHN is an excellent whistler. Some say, it's Haffner. Seriously? His whistling - I wouldn't call it excellent whistling. It was crap.

Sheriff Thomas McAllister did much better. :o)))