There are 2 theories I've read thus far that I'm confident are wrong.
First, the earlier theory that Raymond Haffner is Rosalind Harker's brother doesn't make sense. If so, why wouldn't Rosalind say that Timothy Carter was Red John when PJ brought her into the morgue? That way, she would protect her brother and give PJ the mistaken impression that he killed RJ.
Second, no way Kirkland is RJ. Just way too obvious and easy. I don't buy the convoluted theory that he got plastic surgery, which is why Jason Lennon did not recognize him. I actually think Kirkland is trying to kill RJ for himself, hence his obsession with the case. I think RJ will kill Kirkland in the season 6 premiere. Now, you are wondering, "well then how did RJ know the list of 7 suspects?" I think PJ wanted Kirkland's guys to break in, so he would lead him straight to RJ. However, I think one of the homeland security guys works for RJ and gave the information to both RJ and Kirkland.
As of now I'm leaning towards Thomas mcallister mostly due to process of elimination. I don't think it's brett partridge since he's too young, and I don't see how a lowly forensics guy can wield such clout. I think PJ will start focusing on Bertram, mcallister, and haffner, and then go from there.