Finally I will write my own little theory here. Always enjoyed reading and overall I think this site is an awesome idea. Curious to read all of the other theories. :-)

(Sorry for any mistakes as english is not my native language :-))

So first of all, Brett Partridge and Robert Kirkland are off the list.

I don't really buy into the ideas that Partridge faked his own death or that Michael Kirkland is Red John. Seems too simple for me, and Michael Kirkland is not on the list, which I think is true, as there are just not enough episodes left to have another twist and another twist and another twist in the story.

After "Red Listed" we now know that "Tyger Tyger" is the codeword for an underground government organization, with Reede Smith being a member of it. In "Black-Winged Redbird" we also saw McAllister, Smith and Bertram discussing stuff; which leads to the conclusion that these three are all part of the Tyger Tyger Collective.
They seem to have some connection to Red John. My theory is that the revelation of Red John would bring them into trouble somehow... to quote them in a scene: "How much does Jane really know?".

Smith also killed Kirkland, probably because they don't want Jane to get information from him. I don't know if they know the identity of Red John, but I think they have an interest in Jane NOT discovering who RJ is.

This leaves two names: Ray Haffner and Bret Stiles. 

A lot of things point to Haffner. He likes Lisbon (that would explain why he spared her and just drew the smile to scare Jane), he's a good whistler (as he leaves Lisbons room), he's involved with Visualize (Stiles had information about RJ).In the press release for the "Red John" episode and the episode before, there's an actor listed as "young man". You could say that from his looks that he may play a young Haffner at the Visualize farm back in the day.Haffner also had more appearance in the show than Bret Stiles. I think it would be smart to not pick a character who hasn't appeared in ages to be RJ.

Obviously there are more facts pointing to Haffner at the moment, but there are also some pointing to Stiles.

Stiles has the connections, charisma, mental abilities and intelligence to be someone like Red John. I don't really see these qualities in Ray Haffner. Out of all the suspects on the list, Stiles is the only one I could picture being able to be able to tool Jane like RJ does.

There's also a statement of Bruno Heller saying "we would be disappointed" if we find out who RJ is. This obviously can be interpreted in a lot of ways, but one could surely be: Bret Stiles is the only one capable of doing the complicated, intelligent things RJ does to fool Patrick all the time.

To conclude: I'm really split between Haffner and Stiles. It could be both of them. If I go with the facts I must say Haffner, but somehow my feeling tells me it's Stiles.

Thanks for reading :-)