Gamecube by far. The controls are better and much less flunky (for example, try to perform a Shield Attack on the Wii Version. Half the time you'll get a Shield Attack, and the other half of the time you'll get a Spin Attack.) There's none of that nonsense on the Gamecube version.
Also, the fact that there are more buttons on the Gamecube lead to great things that you can't do in the Wii Version. Three things in particular come to mind: Control over the camera (like in The Wind Waker), being able to hold a spin attack, and being able to instantly, and, without stopping, do a backflip off Epona anytime. No matter what the speed you are going or where you are, you can get off Epona anytime you want.
Also, Link is traditionally a lefty in this (drives me nuts in SS and Wii Version of TP) and the whole world of Hyrule isn't flipped around. Lake Hylia is in the southwest, the desert is in the west, Kakariko is in the east, etc.
And finally, you can control what type of sword slices you do. You can switch at any moment too. You can slash to the left, the right, forward and then do a stab if you want. Also, the aiming and view for things like the Bow and Clawshot is better, in my opinion. And carefully aiming and hitting your target with the Bow in the GC feels much more satisfying, and I just love the first-person view.