Penn is one of my all time favorite fighters, but I've still got to pick GSP for this one. After the GSP/KOS fight, I wrote a post where I admitted that I finally believe GSP is the undisputed #1 WW in the world, and I meant that. GSP is much bigger and much stronger than Penn, and would undoubtedly follow a similar formula to what he did in the last 2 rounds of their first fight. That is, take Penn down and hold him there. I also think GSP has improved greatly since their first fight in all aspects of his game.
I think this just ties into the changing nature of the game and Penn's need to stay at LW. He's a natural LW, and when he moves up to WW he seems to have a hard time staying in decent shape. Even then, he's never going to be a big WW and that in itself is an inherent disadvantage. I feel BJ needs to play it smart and stay at LW, where he'll be a dominant force and be fighting at his proper weight class.
It took till his last fight to convince me, but I finally believe GSP is the true king of the WW division.