So Americ from Happy Cool posted a very good theory about Red John entitled "The Handshake Theory".  In this theory, he points out the handshake had to have been onscreen.  Otherwise, why even bring it up?  I believe this is true.  Sure he could shaken hands with some of the suspects off screen, but would that really be very good story telling?  I don't think so.

So Americ goes through the list systematically to see who Jane shook hands with onscreen.

Brett Stiles- did not shake hands
Brett Partridge-did not shake hands
Reede Smith- did not shake hands
Ray Haffner- they shook hands
Gale Bertram- they shook hands
Bob Kirkland- they shook hands
Sheriff Mcallister- they did not shake hands

So Bob is dead, and Gale doesn't fit the physical description.  Thus leaving Ray Haffner.

BUT

Here's the rub.  We HAVE seen Jane and the Sheriff shake hands... just not in the traditional sense.
They're very first scene together, they play a long game of rock, paper, scissors and Jane keeps winning over and over again...  What do you do every time you play this game?  You shake your hand three times before revealing either rock, paper or scissors.   Thus, Sheriff and Jane "shook hands" the first time they met, just not with each others' hand.  :)  It's a very iconic scene from the first season.  Take a look at the first part of this video to watch it!

http://www.youtube.com/watch?v=0w_Oc5wOeWw