Its a tie between Ocarina of Time and Majora's Mask for me, but i slightly favor MM overall. The stories and game mechanics of those two games were pretty amazing for their time, and i would say they still hold up pretty well today. I also liked Twilight Princess since it felt similar to the other two I mentioned and the whole wolf and twilight concept was something that i really enjoyed.
Overall, I would say Majora's Mask is my all time favorite Zelda game. The game had so many deep elements into it like the feeling of sadness that the world is ending and the depth of the story that made you feel like you were in the game. It was truly a masterpiece.
