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Well, Ocarina of Time has other weapons in this fight too if you don't want to count the 3DS version.

OoT was released on GameCube twice, and it's on the Wii Virtual Console. The GameCube versions however, are special editions; one included in the 'Legend of Zelda Collectors Edition' that you could get via Club Nintendo (in Europe at least, I think in the US you got it by pre-ordering Mario Kart (?)), the other included with the pre-order of Wind Waker.

But alas, I don't think those will be enough to bridge the gap of a million, and it's unfair to include OoT 3D with the numbers. OoT 3D is not a re-release of the same game, but a remake. Thus, Twilight Princess indeed takes the crown as best-selling Zelda game.