For me, it's Majora's Mask (the original, not 3DS remake). It had a dark and (at times) twisted theme to it, something that hasn't been seen since (Twilight Princess dipped into it with the Twilight). The world wasn't the largest, but the 3 day cycle put a spin on how you played (even at times putting pressure on you to finish a dungeon quick (looking at you Great Bay Temple)) The masks providing hidden powers and used to progress some of the side missions was a nice idea.
And it was all made in a short space of time as well, which was impressive.
The 3DS remake made the game more accessible for players, as at the time the game was tricky to follow and to understand without trial and error at times. But for me, it took away part of what made the game great.
Ocarina of Time, Wind Waker, Breath of the Wild and A Link to the Past are very close behind. But to be honest, i've not experienced a bad Zelda game outside of the CDi Zelda and Zelda II
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