It's Brett Partridge, the forensic specialist from the pilot episode and the season 2 finale. I'm not sure if somebody's already laid this out, but here's why:
1) The people who write The Mentalist like to be tricky (which makes some of the episodes predictable since you learn to expect the unexpected), so it makes sense for them to put Red John in the pilot so they can say at any point that Red John has been on the show since the beginning and get people questioning the main/recurring cast.
2) Partridge appears in two cases of murder involving a fake Red John. The real Red John would of course be interested in investigating and eliminating "cheap imitations of his work," and Partridge's job allows him to get close to the crime scenes.
3) The two biggest clues for me are the fact that Partridge has made more than one appearance despite not being a very developed/important character and Red John's voice. Both Partridge and Red John's voice have that weird, nasally quality.
4) I don't remember who Partridge works for, but if he works for the CBI then he could've easily killed his accomplice Rebecca after she killed Bosco's team. It also makes sense how he'd know that the Red John case was re-assigned to Bosco. If he doesn't work for the CBI, then it's even more suspicious that he was present for both the imposter Red John cases, assuming they weren't geographically close enough.
5) William Blake, the poet who wrote the poem Red John recited ("Tyger, tyger burning bright..."), did an oil painting called A Brace of Partridge.
I may be wrong, but I think a huge part of solving these kinds of things are thinking outside the framework of the show and thinking what the writers would do.