I think that red john is Dr Linus Wagner because :

1. Red John doesn't like the copycat and he kill the copycat. Dr Linus Wagner is in prison.

2. Nobody can think that Red John is Dr Linus Wagner since he is in prison.

3. Jane was wrong because the first murder was truly john red. (episode 1 season1)

4. In 1988, red john is 30 years olf or less. In the first episode, Dr Linus Wagner is maybe 55 years old. 

(2008-1988 = 20)
(55-20=35)

In 1988, Dr Linus Wagner was 35 years old.

5. For me, red john is appeared in the first season.

6. As Timothy Carter, Dr Linus Wagner help the children in difficulty.

I'm french, sorry for my bad English.