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.