Seeing as I'm left-handed myself, I much prefer Link to be a lefty as well.

However, I've only played Twilight Princess for the Wii, and I use the controls in the right-handed manner because it feels closer to the N64 scheme for Ocarina of Time that I'm accustomed to. (I don't do it that way to match the visuals.) At this point I think I would find it really strange to play the Gamecube version, because the entire map is mirrored and I'd be going in the wrong direction all the time, even though the Gamecube layout is the 'correct' one.