Look away if you don't want to see how Red John guessed the list. Credit to JJC, I'll try and add to his theory.

In episode 5x16, we see a dead Lorelei Martins... or do we. Earlier in the episode, we see a picture of Miranda Roman who, Lisbon notes "looks just like her beautiful sister," Lorelei. She was killed by Roy Tagliaferro and her body was never found. Remember Dr Towlen Morning's, another Red John victim's, frozen body? We know Red John has the capacity to preserve bodies. The dead girl with make-up and no bullet wound is Lorelei's sister.

Red John guessing Jane's List

At the start of "Red John's Rules," Lisbon has been bugged. That's how Sean Barlow knew Jane was keeping secrets from her, i.e. The Names on the List. She literally annoys Jane about the names from the moment he leaves his attic. This is how Barlow knew that Lisbon was lying in bed thinking about Jane, during the time of the murder.

The talk with Barlow made Jane feel bad for keeping Lisbon in the dark. He eventually tells her Gale Bertram is a suspect. Then Roddy Turner appears, and blah blah blah. Point is, later on the way to the RJ accomplice's house, Jane told Lisbon all the names of the 7 suspects. Then Miriam Gottlieb, arrives like 5 hours late and its nightfall. She went to get the CD from Red John. Red John was making the CD with Lorelei Martins, who is still alive, while Jane and Lisbon waited at the accomplice's house.

Since Lisbon is bugged, Red John hears all the names. Then he tapes the additional details about how he killed Jane's happy memory and led him to the CD, into 1 take along with the names. 

It's no co-incidence Lisbon's happy memory, "my mother feeding pigeons," is the situtation in which Brett Partridge's imposter appears.



From Season 6 onwards, Jane discovers she's been bugged and uses this against Red John. This is how he beats Red John. Patrick, as I have always maintained possesses much more raw intelligence than Red John, who relies on cheap tricks.

I’ve found
some clues that point directly towards Haffner as RJ in past seasons, and also
in this sixth season he gives away some small things (not the spider, that’s
just a silly clue).

 




First I
will summon the most important parts of his first two appearances:

 



                                                  S04E02 Little Red Book          

 



-> The
fake Red John was killed by Jane according to plan, the real one is in the clear now and finally risks
to step out of the dark to meet his antagonist.

  



-> At
the beginning Lisbon tells Jane that Haffner was FBI and very good at
wiretapping & surveillance. Later on, Lisbon is home alone and decides to
investigate the Timothy Carter case a little further. She wants to know whether he was RJ or
not. She calls LaRoche and asks him if she can visit the widow, Sally Carter –
she’s in jail.

 



Next scene:
Haffner is in a panicked hurry and tells Van Pelt (who was reporting about a
case-development) he’s busy. Not very professional of him and it clearly has a
reason. He probably wiretapped LaRoches phone and knows what Lisbon is planning.

 



When Lisbon
arrives at miss Carter’s cell she’s dead (fake suicide & fake letter that
acknowledges Timothy Carter as the real RJ).

 



-> I
also believe in the Heisman clue, which I read about on this magnificent website.
Plus Haffner is lefthanded.

 

 




                                               S05E13 The Red Barn

 



->
Haffner asks Lisbon to join his private project. Though the really important
question for him is how much the CBI knows about the Red Barn murders from 1988.
By asking about the names on Cooper’s archive-list he gives himself away. First
he looks relieved when it turns out his name isn’t mentioned in Cooper's info. But it was
impossible for him to know about this information, unless he’s Visualize
himself, a connection Lisbon easily makes. Haffner talks himself out of it as
best as he can.

 



This must
be a VERY loose end from 1988 when RJ was still young and careless, because Ray returns at the end and is upset the mother and
daughter will only go down for one Red Barn murder, instead of all three. Haffner
claims he speaks for his Visualize-clients, not for himself. Lisbon gets even
more suspicious. Ray, were you there? – Why would you ask me
that? We’re still friends, right?  Lisbon apparently forgets to tell Jane about this. 

 

 




Haffner
returns in the current season. Not in the first episode, but Lisbon & Van
Pelt put GPS trackers on the suspect’s cellphones, which is his MO (remember
the wiretapping). Easy for him to use it against them.

 



                                       S06E02 Blackwinged Redbird



->
Lisbon’s dream. Her subconscious tells her something. Haffner betrays her and
attacks her. For Teresa he has always been the most likely RJ suspect (she
clearly has a better intuition then Rigsby and Cho, who are both betting on
Bertram).

When she
wakes up from her horrible nightmare, Jane calms her. A nurse passes by and
asks for Carmen Lee. This looks like an indirect way for Haffner to check if
Lisbon is all alone.

 



-> A
little while later he walks in. Lisbon fears him, although he tries being
charming (other than most women Lisbon reacts in a distant way on male charms,
she does that with Patrick & Mashburn too – at least before she ends up in
bed with him). First he checks if she remembers anything. Then he asks about
Red John again. Why do you care? – I don’t
care. I have clients who care. The clients again. He doesn’t
like her questioning. Before leaving he states that someday he and Teresa will
have the time, as saying the last time (when he knocked her out on a creepy location) they didn’t
cause something came up.

 



-> RJ’s pseudonym
when visiting Sophie Miller was Jay Roth. I supect Haffner of having German
blood for historical reasons, so a possible connection. Although this isn’t a clue - just a personal
hunch.

 

 




                                              S06E05 The Red Tattoo

 



-> Strange
episode. Why would RJ use a spy, especially such a fudgy one, to bug the CBI? And
if Haffner is RJ, it wouldn’t make sense at all because he’s the master bugger.
So must be a trap.

 



->
Finally we see one of Haffner’s “clients” with our own eyes, and then that
client is simply Cooper, the errand-boy of Visualize. His contribution to the
whole case is pretty useless + he failed to protect the dead guy, who also was
a client of his. Two possibility’s: or he’s a useless cop (which would
contradict Bertram’s & Lisbon’s first opinion of him in season 4) or he ain’t focused
at all (which would mean he’s all about the RJ case again).

 



->
Haffner meets Jane in the elevator. When they leave, he tabs on Jane’s shoulder
and tells him there’s a comeuppance coming his way. Jane replies you’re even a worse psychic than you’re a
cop.

So if he
wanted to make Jane believe he’s a bad cop, it definitely worked. But indeed, this
is a silly prediction also by Haffner. Unless…

 



-> He
gets the autopsy-report of the stabbed man before Lisbon. He claims that he
still has friends in CBI, they help him if he needs it. Maybe Bertram is his “friend”,
since he also knows that Jane riled some very powerful people (later on he advices Teresa & Grace to step away from Jane's tricky business).

 



-> After
Jane solved the case, Lisbon asks Cooper where Haffner went. He had some business to attend to. I am not his only client. Haffners
vague client-alibi again.

 



-> …
unless he had it all carefully planned ahead. And he already has the gathering
of the 5 remaining suspects in mind. Would be a nice trick if he foresaw Jane
finding out about the spy being RJ’s, and very well timing to assault her just
before police arrives. Best part of the trick is to let her live for a few
moments and make sure she mentions the tattoo, which was easy to fake (I mean,
three simple dots?). Now Jane is unwittingly going after the Tiger Tiger clan
instead of him. RJ allready killed an important member of that clan in the person of Partridge, whose task it was to make some Tiger murders look like RJ killings, even maybe Lorelei's. It's possible he wanted to lure them Tigers out by taking away their forensics expert. 




 

 

                                             S06E06
Fire and Brimstone

 



-> For
the first time we hear Ray making a call with a real client, about a woman that
needs to be kept quiet. When he meets Teresa in a coffee bar, Lisbon can’t
help showing through she suspect Haffner as RJ. He now acts very well: not much
hesitation, just pretending angry and determined about it. You wanna question me you arrest me. An innocent man would, despite
of liking her very much, now detest Lisbon for good. But he kind of forgives her
immediately. And sticks with the plan. He wants to see how Jane will lay focus
on the wrong guys.

 



-> After
Jane tricked Lisbon and leaves her on the side of the road on his way to Malibu, the first car she
lifts for drives trough. It’s a Mercedes, and possibly the same Mercedes
Haffner drives. If it’s him, he off course will stop for no one, especially not
Lisbon, because at this point he cannot derive from the trap he (and not Jane)
set up. This is no real clue, more of a feeling it was him.

 



-> Once in
the house in Malibu RJ has to make one important move: make sure the Tigers get
rid of their guns. So he stands up (I don’t
have time for this crap) and forces Jane into taking the riffle and disarm the rest. Now his
real targets, the Tigers, are suddenly in a very vulnerable position. He is laughing at the inside, because Jane is dancing as his perfect puppet.
Maybe Jane has a counter-trick planned, we’ll that see in the next episode.

 

 




So, to
conclude: if Haffner will turn out NOT to be Red John, I’ve been misled very
well :) 
Though I can't help but imagine him sitting across Jane in a quiet place, saying oh, why do people always call me Red John
anyway? That’s just a stupid name, isn’t it?

         

I think we've exhausted the theories on who Red John is based on evidence, so here's my theory on how Jane catches Red John based on evidence...

Jane chases Mcallister into the Park. Dumps muffins all over him and he gets mauled by pigeons. Mcallister has panic attack from his fear of pigeons and faints. Patrick Jane ties him up and holds him down. Tom wakes up and Jane slices him up. End Scene.