I thought it was interesting that Ray Haffner whistled "Jimmy Crack Corn and I Don't Care" as he left Lisbon's hospital room.  Of course, the next words in that song are "My Master's Gone Away."  

It got me to thinking that Ray Haffner may not be Red John after all.  He could have whistled anything.  Why did Heller have him whistle that?  This is not necessarily saying I think he is innocent, however.  

Another interesting observation with regard to the words "Tyger Tyger," spoken by a dying Partridge. Yes, this refers to the poem; however, could it also be referring to the fact that there are two "tygers?"  Father / son, perhaps? 

Bruno mentioned that there is a secondary "duplicitous" situation occurring simultaneously, along with the RD hunt.  I think this is what Sheriff McAllister, Reede Smith, and Gale Bertram are in  Bertram's office discussing, I believe.  As a result, I exclude all of them as suspects.  Brett Partidge is dead, so obviously he is excluded.  That leaves Bret Stiles, Ray Haffner, and Bob Kirkland.

Thoughts: 

Bob Kirland has the right tonality for the voice of Red John.  He also has the ruthlessness to be Red John, as evidenced by his killing someone to silence the fact that he could identify Red John.  
Bret Stiles:  Has the power and ability to control/manipulate people.  However, his age gives pause to consider him to be RJ. 
Ray Haffner:  Possible.  He seems a little sweet on Lisbon.  Could this be why she was not killed?  And what did he mean exactly when he told her that they would "have a time" when he was in her hospital room.  That seemed like odd wording to me.  And the name Ray is close to Roy.

Could Bret Stiles' son be RJ?  Could that son either be Bob Kirkland or Ray Haffner?