Ocarina of Time. It still holds a great deal of nostalgic appeal for me, and will always have a special place in my heart as the Zelda game that introduced us to Link's voice. If I'm being totally honest with myself, though, I have to admit that it is torture to play today. The graphics I can forgive, as I've never been one to dismiss a game for its visuals, but the awkward, not-quite-there controls just kill it for me. Every time I try to go back and replay it, I end up replaying Wind Waker instead.
Hopefully the upcoming 3DS re-release will rectify this.