To address deeman first, I don't think Pena is an option at 1B, because apparently they tried him there on his rehab assignment in AAA this year. The only result I heard from that experiment was: "The experiment ended quickly". I assume this meant Wily was atrocious at 1B as well.
This is the problem of having 3 DH's on the team, and yes, I realize there are worse problems to have than seeing Ortiz, Ramirez, and Pena in your everyday lineup. The focus here is defense.
To address Misfits post, I don't think you can enter 2007 with your defense in right field resting on learning how "read balls off the bat better" and making less mental errors. Maybe if they have the guy practice every day of the off season, but isn't reading balls off the bat more of an instinct type of thing? Why has Pena not learned to read balls better off the bat so far in 2006? I just don't think you can expect Pena to improve that much defensively as he's been in the big leagues for what, 4-5 years now? To me, what you see now is what you are going to get.
I'm probably sounding harsh on Pena here, but I am strongly opposed to seeing him as the starting right fielder in 2007. I really think it will hurt the team. Obviously, you can not move around Ramirez and Ortiz so I say they decline to offer Nixon arbitration (obviously), trade Wily Mo, and sign Carlos Lee! How crappy can Lee be in RF?