I actually started getting paranoid about Bertram when he referred Red John's lines in S2, but the actions of Stiles makes me feel that it is indeed he who is the real Red John.
Stiles couldve told his disciple to go shooting the killer of his lover outside the CBI, and then when questioned, he could say he felt that was right as manipulated by Stiles...S3 E3

But there are other points that also make Stiles a lesser suspect. But Im jus pouring some extra juice into this investigation!!

Kindly do check out my review of The Mentalist at my blog http://lifethearsway.blogspot.in/2012/09/series-review-mentalist.html and pass the word on if you liked it!