Have a good look at the picture, you'll noticed the game is different.
In the standard edition, the game is just a standard copy of the game.
In the special edition, the game is the special "limited" edition (read: collector's) of the game. Here's a link to the special edition game by itself...
Actually the original Nintendo 64 version is available as a Wii (original) VC (Virtual Console) title isn't it? I know it's a Club Nintendo prize this year. And it shows up in the Nintendo game list: http://www.nintendo.com/games/detail/7OfVrKE-E5ri9Rjnqx9FBs0gIzJGZtns
And from what I read the...
I just cleared the Great Bay temple, and the fairy reward was the defense upgrade. I think this was the same as the N64 version. Last one is the fairy sword.