Everyone seems to think that Red John is taking Jane on a journey, but I think it is Jane that is taking RJ on a trip.
I think Jane knows who RJ is.
If you watch how Jane works, he often designs a trap for the perpetrator. 
Jane often plays along with misinformation to lead the perp where he wants them.
I don't believe that RJ is on the list of 7 suspects-Jane set this up. 
I believe that some of the people on the list of 7 are complicit with Red John, which is why Jane doesn't get upset if they die.
I don't believe the clues on Sophie's recording to be completely true-I believe that Jane got Sophie to make the recording to help set a trap for RJ.
I think Jane will use some of the suspects as part of his trap.

That is all I have at the moment.

What I know for sure:

I would like to see Mashburn again-(and I think he might be RJ).

I would love to see Jane reclining on that sofa in his underwear.
New mystery to be solved: Boxers or briefs?

In Season 1 Episode 23 , Rosalind Harker wrote RJ a letter saying she found this address on a buisness card down the back of the sofa, how could she do that if she is blind? You may say RJ planted the letter and Rosaling knew nothing about it, but Jane said to her "in the letter you wrote him you said he was cruel to you" and she acted as if she knew about the letter. So either Bruno Heller messed this scene up on accident(highly unlikely) or Harker is not being truthful about RJ's identity. Harker said Roy smoked alot, none of the suspects have been seen smoking if i am not mistaken? But dumar, the cop who brought the elephant, matches the description she gave of Roy, so maybe she never met RJ and only Dumar? Or perhaps she is lying about everything.

Also is Strawberries and Cream pt 2, how did Timothy Carter know that Jane and Bertram would be in the mall? Jane would of told Bertram in the car where they are going, so maybe he sent a text out the Timothy? Also after Jane had the meeting with Bertram, Bertram picked up the phone and the scene changed so we didnt see what he said, maybe he rang carter, told him to park outside the CBI, and follow Jane's car when he leaves with bertram? If this is what happened , RJ is Bertram.

But i doubt this for some reason, and none of the suspects really stick out to me as RJ , so i dont have a suspect for RJ.

All the main suspects are Red John.'Red John' is the name of a serial killer order, cult you name it.

If you watch the newest episodes one thing becomes clear: the list of 7 suspects does not contain Red John. All 7 suspects are loyal to Red John and are pressuring Jane one by one so that he becomes more paranoid, just as Red John wants. Therefore, he is able to keep tabs on Jane's actions and reactions through these suspects and it is why he knew that Jane would end up with those 7 names because he planned it.I also believe that we have not yet met Red John; he is someone that Jane does know but we do not. It is possible that Red John is in fact someone from Jane's earlier years and thus we don't know that person yet.Finally, I think that all of Red John's previous victims were just ways for him to gain the interest of the police and hire Jane. I think that Red John was targeting Jane all along and simply using victims to gain fame and be known; therefore, once he had Jane's interest he began to toy with him and play him.

New updates for the investigation.

See the new compiled facts and associations here (Google Documents spreadsheet) https://docs.google.com/spreadsheet/ccc?key=0Aus4cbInagyBdExtWDJWVDRjNDRSXzBqMWpvVDBEV0E&usp=drive_w....

Do not hesitate to copy the sheet "copy of public" (little arrow/bottom right of the tab) to analyse your theory and then contribute to the investigation in the sheet "public"

The thing that always intrigues me, ever since 5:13, is what happened between 1988 and 1998? The Elliston farm murders (likely committed by RJ) happened in 1988, yet Red John didn't officially start for another decade. So what was he doing in that 10 year period, and what happened to him? 

If he went 10 years between his first few murders, and then became a notorious serial killer, it suggests one of 2 things:

1) Someone else committed the 1988 murders, and the smiley was just a graffiti incident that happened to take place on the same farm. RJ did the graffiti, but not the murders, or was inspired by the graffiti

2) Something seriously bad happened to RJ in that 10 year window, something that changed him from someone who killed 2 people probably out of deep personal loathing and self preservation (they weren't very pleasant bosses, drugging their workers and working them to near death), to a man who killed for personal pleasure and fame.  

Your average serial killer will kill, then keep killing until they're caught, no 10 year breaks.

Hopefully all will be explained in 6 weeks, because it's been bugging me for a while, and i'm yet to find a logical reason for the change in behaviour from 88 to 98-present day

If anyone has answers, comments would be appreciated.

Heller said:"There is a clue buried in that final sequence that will pay off big time
in the finale of the Red John story. A very big clue. No one will get
it from the clue as it is laid out in the episode, but it will pay off
later."

Sophie Miller says that jay roth has a phobia maybe achrophobia (fear of heights)
she's not sure about it.

then I thought of what patrick told lisbon in the hospital about why rj didn't kill her.He said:" Maybe something spooked him and he couldn't go through his usual routine"
Remember what was in that house in first episode?PIGEONS
Lisbon left the door open so pigeons could get out of the room.
that is the big clue heller told us about IMO.RJ fears pigeons
in fact at the min.28:59 we see someone feeding pigeons and patrick staring at them