So it's already been said, but the game is flipped. To be fair, the game started as a Gamecube game and was ported to Wii. But the entire world is a mirror image. If in the wii version a door is on the right, it's on the left in the GC version. So if you're using a guide or walkthrough, make sure you're looking at the correct version. And Link being left handed is a character trait that was blasphemy to remove...this is coming from an actual left hander.
- The Wii version uses the Wiimote, which means it has a totally different control scheme. One advantage is that this allows for more accurate aiming with the bow and arrow.
- The Gamecube has free camera control, whereas the Wii version does not
- There are three slots for items in the Wii version, whereas the Gamecube version has only two
- The Wii has a widescreen 16:9 option, whereas the Gamecube only allows for 4:3
Other than that, they are pretty much the same. The Wii version is a hell of a lot cheaper, but if you're like me, I hate the wii mote (and motion controls in general) and would rather play with a standard controller. The Wii version MUST use the wii mote and nunchuck, no alternate controllers allowed.
There's also little stuff, like being able to use your shield on horseback, rotate the c stick for a swing attack and growl as a wolf by pressing B. All these are GC exclusives. Minor stuff, and kind of pointless, but it feels like a more controllable and interactive game. IMO.