It's a close call for me between John Shea and Michael Rosenbaum. They both had a lot of the qualities that I enjoy most about Lex. They were both very good manipulators, they could both be charming at times while still ultimately being ruthless when you get right down to it, and they both were businessmen, the version of Lex Luthor that I tend to enjoy the most. That's not to say that any of the other versions of Lex aren't valid or good in their own right, but John Shea and Michael Rosenbaum just fit my own personal tastes the best. It's hard to pick a favorite between the two of them, but I think I like John Shea's portrayal just a little bit more.
Gene Hackman is easily my third favorite Lex Luthor, though. He did a good job at bringing a little bit of humor to the role. His scenes with Otis were particularly amusing to me.
Since we're on the topic of Lex Luthor, I'd like to give a little bit of insight into my own personal experience seeing one of the actors who portrayed him, Michael Rosenbaum, in person. Last summer when I visited Metropolis, IL for the Superman Celebration, Michael Rosenbaum was one of the celebrity guests that attended the event. Based on that experience, I can tell you that he is without a doubt a very funny man and really knows how to work a crowd of fans. He requested a wireless microphone during the Q and A so that he could move around and walk among the fans. None of the other celebrity guests did that. Sadly, I didn't get the chance to actually meet him, but he was standing about two feet away from me at one point during the Q and A session, which wouldn't have happened had it not been for him moving around the crowd, as I was standing at the very back of the crowd.