Well that is a very tough one.
Wind Waker is the game I feel the most nostalgia for. It's timeless beauty and huge mysterious world make it one of a kind, and a game that I really really care about. That sounds incredibly melodramatic, but no other game captures my youth like this one. I remember playing it for hours and hours.
But then there is Metroid Prime/Super Metroid- These games are both better than wind waker, and I enjoy playing them more. They don't hold quite the place that Wind Waker does, but they are very close.
It's hard to choose.