My 3 favourites are:
1 - A Link to the Past (love the game but mostly just #1 for nostalgia)
2 - Breath of the Wild (Objectively the best one in virtually every way)
3 - Wind Waker (Best music, story, and characters, second best art direction)
beyond those three it gets kind of muddled. II and Skyward Sword are at the bottom (not counting the CDi games), Ocarina of Time is simply okay, most of the handheld games are good but not great.
I got it all, baby!
PS4, Switch, WiiU, XBO, PC
Vita, 3DS, Android
Top 6 this generation:
Bloodborne, Sekiro: Shadows Die Twice, God of War, The Legend of Zelda: Breath of the Wild, Dark Souls III, Red Dead Redemption II