Questions that need to be answered:-

-Who is Red John?
-The "He Is Mar" clue.
-What happened at that house the night it blew up?
-How Red John knew Jane's list before he did?
-How did Red John kill Jane's happy memory?
-How was Red John always one step ahead of Patrick Jane?
-Why did Red John tell Patrick the poem of William Blake? (Why does he want him to know about the Blake Association?)
-Origins of the Blake Association.
-Why didn't Jane take Rosalind Harker's description of Red John into consideration before making the list?
-The Kirkland twins.
-Why did Red John kill Bret Partridge?
-What Brett Stiles meant when he said "I know more than you or Red John could ever know".
-Why the hell CBI Ron was in so many episodes?
-The freakin' pigeons!
-How Red John has so many accomplices that are willing to do anything for him?
-Red John's voice
-Who poisoned Rebecca?
-How did Kristina Frye become the way she is?
-How did Red John know about "Roll Tide"?
-How did Red John become Red John?
-What was the big clue at the end of S6E1?
-Why did Red John save Patrick? 
-Who burned Todd Johnson's body? (Possibly Craig O'Laughlin)
-Why were Bret Partridge and Todd Johnson's last words "Tyger, Tyger"?
-What did Bosco really say to Patrick before he died?
-What is the deal with Kirkland and Alexa Schultz



Agree? = GREEN

Let me know if I have missed any more in the comments.