Have you'll noticed that Lisbon's cast is on at the beginning of Season 5 the last episode Red John Rules. And at the beginning of desert rose. But her cast is off at the last scene when she went to investigate Brett Partridge at the house. Lisbon is up to something. I believe that is one of the clues Bruno is talking about. The small little details. Plus Lisbon never told Jane what happened to her wrist when he asked about it.

Lisbon is Red John. She is an excellent actor and has been manipulating Jane from before he even met her. She is completely in love with Jane and perhaps fell in love with him when she saw him on TV. She uses her position as Jane's closest friend to be close to Jane and strings him along, relishing the time they spend together. To her they are living a happy life together. She thinks that no one knows she is Red John, and Jane suspects her but is conflicted about it as his suspicion grows. 

She has another accomplice or many in the CBI. Rigsby is likely one of them. Lisbon thinks that he doesn't know that she is Red John, but perhaps he suspects she is or even knows. Grace who may or may not  be a disciple of Red John, unaware that her coworkers are accomplices, will be Lisbon's trump card against Rigsby, who like Jane, might also be after her for his own reasons, maybe for revenge or to "become" Red John.

If Rigsby is an accomplice to Red John he will likely kill Cho. Jane will set a trap for Lisbon, but Rigsby or some other accomplice will mess it up. Jane will be "fatally wounded". Lisbon will confess her love to Jane and he will actually die but catch Red John by recording her confession or having it witnessed.

before lisbon enters the house, she is waiting outside, we hear a car drive by, she stares at the car (which we never see) for a long time time as it drives away, like it's familiar to her, then she hears a noise inside and enters the house. 

early in the episode Lisbon had a cast on her right arm, had to shake hands with the officer at the crime scene with her left hand. In the last scene she did not have a cast on her arm, holding both the flashlight and gun. weird....why? she knows more than she is letting on.

Okay. Not accusing Lisbon of being Red John, but I found it very odd, that none have noticed the weird detail in the slow-motion scene in the ending of the "the blood on his hands" S03E03. We see our four agents walking towards the camera, in slightly different directions in slow-motion. At last our dear Lisbon - but notice, that after her, another woman with the exact same look (apart from the ponytail) walks the complete opposite way. The suit is the same, the face and bla bla. This can't a camera-mistake cause of the hair differences, and why put a strange random person in such an important and dramatic ending...
Could this be a symbol of a "two-sited" personality, of a secret personality or a way of showing that she is loosing her way? If none of these what then? I don't think this is a coincidence...

Do you guys remember Sophie Miller....? 

Jane told to Lisbon alone that she (sophie) helped him after the death of his wife and daughter.

I strongly think that Lisbon is accomplice to RJ.. 

Lisbon passed on the info about sophie to RJ...RJ wud ve easily got all the happy memories from her using his skills....and that is why RJ came to know about Jane's happy memories...

End of story....

Why would Lorelei tell RJ that she told PJ that RJ and PJ shook hands , i mean Lorelei hates RJ now , because RJ raped and killed her sister,and in the RJ video RJ said "Lorelei told me what she told you about shaking my hand" , because he wants to cover on who ever told him which is Lisbon , because Lisbon is the only one who knows that Lorelei told PJ that RJ and PJ shook hands .I need an explanation