1. Spirit Tracks. I recognize that there are better Zelda games, and I myself have some grievances with it; namely that the spirit flute has to be by far the worst Zelda instrument. But the things work about this game are done amazingly well and easily more than make up for its faults. I really like the train, and I love Spirit Zelda: having Princess Zelda be Link's adventuring companion in this game was nothing short of brilliant, to the point where I almost wonder why it wasn't done sooner and I do wonder why it hasn't been done since. Controlling Link and Zelda together is a ton of fun.
2. Ocarina of Time. It introduced me to the Zelda series, so of course it's going to be in the top 3, and it helps that it's still one of the best Zelda games overall.
Nominations for 3rd place: Link's Awakening, Majora's Mask, Wind Waker and Breath of the Wild.
Winner of the position of 3rd place: Wind Waker. There isn't really much to say; like Sprit Tracks, the game has a ton of charm, the sailing is fun, and I really like the deep narrative under the surface and the theme of the winds of change and the idea that Hyrule waiting for a hero to appear was exactly what doomed Hyrule.