Some observations on my part:

for starters, I think the idea of the list as a plot element is very good, it helps build suspense and anticipation of the final reveal. But for me, the list is poorly done. From what I saw in the show, right off the bat I eliminated Kirkland, Stiles and Smith, then Partridge was killed off in the season premiere so really 45 minutes into the list of seven and we're down to three. I thought the list should have consisted of more exciting names, or basically just characters that don't make you write them off immediately. This format of going from one suspect to the next in each episode is wrong because it takes away a lot of the suspense, and in my opinion ordinary murder investigations just get in the way of the main story arc.
Also, I think Red John is on the list. I like what someone said in one of the theories, that we shouldn't overthink and overanalyze. Heller said we could trust the list so assuming he isn't blatantly lying to his own audience (he could have just kept quiet), we can expect RJ to be one of Bertram, McAllister and Haffner. And I don't understand why people assume the list is fake, or a trap of some kind. Unlike the list that Kirkland had stolen, this one was in Jane's head, and Red John somehow managed to come up with the same names.
As for the way Jane narrowed it down, I think it was weak and far-fetched. Out of more than a thousand people whom he had shaken hands with, he eliminated all those who couldn't have commited the Red John attributed murders. I find some things very shaky with this line of thinking. For one, the assumption is that RJ actually did commit all of the murders he's suspected of, Note here that getting only one murder scene wrong would be enough to leave RJ off the list, not to mention the fact he could have had a disciple do some of the killing. But now comes the really incredible part - Jane was somehow able to remember the whereabouts and alibis of dozens of people for the RJ murders. This begs the question how Jane would even go about finding all of this out, particularly considering Lorelei told him about the handshake fairly late in the game. Just doesn't seem plausible at all.

I noticed that quite a bit of theories here focus on the fact that a certain actor is listed in the episodes revolving around Red John, and so they have to be the primary suspect. I disagree with this because it should be easy to leave a name out of the cast list. Imagine you are Bruno Heller, you and your writers invested time and energy into closing the RJ story arc, only to have it all blown wide open by the simple fact that IMDb lists some actor for the Red John episode. Something as simple and irrelevant as a cast list should not play a part in one of the bigger reveals in recent television. If Heller really allowed such a blunder and it turned out you can actually guess Red John's identity simply by looking at the cast list for 608, then I will have no words. 

I thought the show was rather poorly written and I haven't changed my mind watching the current season. There are, as always, tons of clues spread around randomly, only to thow us off, and the problem is that some of them are forced and completely implausible. For instance, Haffner and his whistling in Lisbon's hospital room. Your colleague, whom you supposedly like, was injured in the line of duty and left at the mercy of a ruthless murderer, you visit them in the hospital and afterwards almost go out of your way to whistle as you casually stroll out of the room. Give us some credit, Bruno. It's so out of place and unnecessary. Then there's McAllister's supposed fear of heights and pigeons and whatever. I just hate it when the show stoops to these lows.

There are some very nice theories here and I enjoy reading the site, but sadly The Mentalist is mostly in The Killing mould, meaning we can't really draw any strong conclusions based on known info, we have to wait for them to show us who did what. And I seem to be in the minority here as I consider the Tyger Tyger organization to be a nice plot point, it adds to the dynamic of the show if done properly.

Looking forward to new theories and finally closing the Red John case.