First let me say that it would break my heart if Lisbon turned out to be Red John. I don't want "Jisbon" to happen (the Jisbon fans kind of piss me off, and a mid-series romance between them would kill so much of the character and drama of the show we love), but because Teresa has, up to this point, been the only real sympathizer to Jane and is perhaps his only "friend".
That said, I could totally see it being Lisbon, because it would be the tragic end to it all, and would present Jane with the most dramatic choice possible for the series--to have to kill the women he secret really loves, his only friend, because she turns out to be the serial killer who murderd his family and drove him to miserable desperation. From the perspective of writing gripping drama this would be the best move I think, and even if Lisbon doesn't end up being Red John, I still think that she will at least emerge as a suspect before the series ends. As a writer, how could you resist this??
But working within the framework of the universe of "The Mentalist", Lisbon raises my eyebrows. This has mostly happened because of the last couple episodes of season 5.
The Broken Arm/Wrist - I'm not motivated enough to find out whether or not Robin Tunney broke her arm/wrist in real life, but I think it's safe to say that they wouldn't have made a point of pointing it out, and have Lisbon brush it off really quick unless it was going to tie into the plot of the show. So, this casts suspicion on Lisbon for SOMTEHING. No, not necessarily Red John, but you'd think that she would have explained herself it was innocent. Presumably Jane knows when she is lying, so perhaps he saw some falsehood and really felt like he shouldn't press the issue. Perhaps Jane is suspicious of her.
Lisbon's Continued Survival - Red John has already shown he has no problem murdering the people Jane holds most closely. He's killed Jane's family, and his "happy memory". It's obvious that Jane has special feelings for Lisbon (whatever they may be), so why not take Jane down another peg and remove his only friend?
No theory is air-tight. In writing the above 2 points, I am already thinking of a bunch of counter points which should discount Lisbon as RJ. But that's the whole thing--we're not supposed to know! Maybe even Bruno Heller doesn't know yet! haha. Every plausible theory has a plausible counter theory. That's what makes this a good show, guys - we're kept in suspense and drawn into the drama!