Let me share some possible clues I've found.
Season 1
1) In S1E1 Partridge believed the crime was made by RJ, which was a mistake. This reduces his chances to be RJ.
2) In S1E11 "He is Mar..." was on the hotel wall. There is no sense to write a surname (like Mars or Martins), because there would be no "He is" before it. So "Mar..." is something else. The most probable guess is "Marshall", which may refer to almost anybody from the final 7 list, except Stiles,
Season 2
3) In S2E8 an officer poisoned Rebecca (Bosco's secretary). Her smiling reaction directs to the conclusion that the officer was RJ. This speaks only against Stiles to be RJ.
4) In S2E23 RJ reads Blake's poetry to PJ. I see no reason to do that. The only thing might be to make PJ suspect somebody, who likes Blake (but as this point we hadn't met Bertram yet). By the way, RJ may be creating suspects by giving wrong clues ("He is Mar...", "Tyger...", else).
Season 3
5) In S3E3 O'Laughlin, while working on visualists' case, lets a guy shoot the member who was going to provide evidence against Stiles. So the man who was working for RJ worked for Stiles.
6) In S3E3 Stiles passed to PJ information about Frye. Can't make any conclusion from this yet, but obviously it's an important moment.
7) In S3E9 Todd Johnson's last words were "Tyger, tyger". After being burnt by O'Laughlin (and so by RJ), Todd would like to say something very important to PJ. So either Todd wanted to say that it wasn't RJ in S2E23 saving PJ, but Todd himself, or Tyger is a clue leading to RJ's identity. The only real thing is the letters "TYGER" or "TIGER" (this variation is also met in literature) being in the name and/or surname of RJ, for example "parTRIdGE".
8) In S3E16 Bertram directed LaRoche to suspect Hightower, which was a favorable scenario for RJ.
9) In S3E16 Bertram quoted Blake's poetry.
10) In S3E23 Gupta said he was very religious. This is a Stiles direction.
11) In S3E24 Timothy Carter (fake RJ sent by RJ) was at the mall cafe. So who did know about the meeting? Bertram knew. Besides, RJ knew about the "hotel floors trick" (because RJ sent Carter). So in the list O'Laughlin should not be the only RJ man. And again, Bertram is the primary candidate.
Season 4
12) In S4E1 Bertram asked the attorney to enlong Timothy Carter's case and probably was sure Carter wasn't RJ. This brings some increasement for Bertram's chances to be RJ.
13) In S4E13 RJ is shown to be left-handed or at least "equal-handed". Watching different scenes brings to the conclusions, that Bertram, Haffner, Smith and Partridge are right-handed, while Kirkland may be left- or equal-handed with a high probability. No valuable scenes found with Stiles or McAllister.
Season 5
14) In S5E1 Bertram tried to save Lorelei at CBI and not to pass to feds. This may be interpreted both as a RJ behavior and not RJ behavior. Anyway this may be a clue.
15) In S5E5 Alexa Schulz phoned Minnelli by Kirkland's request. The first idea is Kirkland to be RJ, but I would prefer another theory: Kirkland was trying to find RJ himself or to prevent PJ from engaging in RJ case and so saving him (see the clues below for more prove of this theory).
16) In S5E6 the transporter-cop told that a fed man called him and organized Lorelei's transfer. This was not to kill her and not to free her (none of these two happened). So the goal was either to interrogate Lorelei (this is a Kirkland behavior) or to put her far from PJ (also a Kirkland behavior).
17) In S5E7 Kirkland told Lisbon to stay far from Volker. Not an RJ thing to do, right? So Kirkland wanted to save Lisbon. What a kind guy!
18) In S5E13, which was about the case of visualists' farm bodies, it's mentioned that Martin Talbot said that a kid painted the smiley on wall. So nowadays the "kid" must be 30-50 years old. Not Stiles.
19) In S5E18 it's revealed that Kirkland knows RJ's identity (no question was asked about RJ before making the deadly injection).
20) In S5E19 Kirkland stole the results of PJ's investigation. But those results were probably fake, as PJ predicted the robbery.
So, let me conclude one by one.
Bret Stiles - Excluded due to his age. An alternative is that Talbot lied about the "kid" to prevent further investigations.
Gale Bertram - A lot of evidence talks for this candidate, but there is no sense in the manipulation with Blake's poetry. Mentioned above clue #14 is also a probable reason to exclude Bertram.
Raymond Haffner - See no reason to exclude him (except the clue #13, which may be not a hard one actually). To be honest, I can't see him being RJ because of S5E13, in which Haffner tried to get information from Lisbon about visualists' case by HIMSELF. Not an RJ style action.
Reede Smith - The same: see no reason to exclude except the clue #13. Actually the main reason to suspect him is his name. Which is the most famous fake name? John Smith (Red John, Reede Smith).
Bob Kirkland - Excluded. A very interesting character, but obviously not RJ. The first reason is clue #16. The second and more valuable is the fact that the disc record with Lorelei which we see in the last episode is made BEFORE Kirkland broke into PJ's room (combined with clue #19, Kirkland just wanted to find out how far PJ succeeded in his investigation). So, I Kirkland might be an ex-victim of RJ or an ex-companion. Anyway, Kirkland wants revenge. The "do you recognize me" question leads to the plastic surgery theory. So Kirkland may be Carter Peak somehow survived. Or Kirkland may be himself in the flashback scene, but later replaced by Todd Johnson. Martin Talbot may also be connected to Kirkland. A little fantastic, but it never seemed that Kirkland is a bad guy.
Tom McAllister - If taking under consideration only fact and forgetting that we are talking about a serial which should have its drama and special logic, I would say McAllister is the most probable suspect. There is no single reason to say he is not RJ.
Brett Partridge - If the series were to finish in season 1 or 2, then Partridge should be RJ. I think he was something like a plan B in case the project isn't prolonged for a new season. But after 5 seasons he's not going to be RJ. Not many facts to prove it, but the very first clue is reasonable.
So, the least possible suspect is Kirkland (only 2%), then comes Stiles (about 6%), nexts are Bertram and Partridge (12% each). Top three opened by Haffner (18%) and Reede (20%). The main suspect unexpectedly is McAllister (30%). He was nobody before the last episode, but now we should expect all the seven to be key characters in season 6, so it's actually not reasoned to say "he's not common enough to be RJ".
Everything said above is based on the belief that PJ's list is true.
