If we aren't counting Zelda I and II which I don't consider Zelda games really I'd probably pick Twilight Princess. Probably one of the worst Zelda games IMO and it's even a bigger let down since it's a 3D title. The only part I enjoyed about those games were the dungeons.
I'm shocked that people are saying games like WW, OoT and TP! those are the games i find myself replaying the most! My answer would be AoL. I'm struggling to get through it once and i can tell i will not want to play this again