Patrick Jane is Red John.

Actually he became Red John when he killed the original Red John at the end of Season 3.
That really was Red John, and Patrick really did kill him.
Then Season 4 reveals that it wasn't really, perhaps just an accomplice.

I believe that the act of killing RJ caused a psychotic break in Jane, creating multiple personalities.  And Jane became Red John.

It's a common theme among cop shows that Revenge is a terrible thing, and it never really satisfies you.