1) Ocarina of Time
2) A Link to the Past
3) Tie between the first The Legend of Zelda and Wind Waker
People saying Wind Waker was not hated are wrong, there was so much hate and disappointment among Zelda fans when it was shown for the first time with the cartoony graphics, specially because a year before Nintendo shown an epic demo of Link vs Ganon with "amazing" graphics.
I think it has a lot to do with your age and circle of friends, maybe younger people were ok with the graphics or didn't have discussions with their friends. At that time I was 18-20 years, most of my friends already moved to Sony console and called Nintendo kiddy. I tried to convince them it wasn't but things like GameCube design or Mario Sunshine weren't helping.
Wind Waker was the final nail in the coffin, when I saw that I was like "oh sh*t! My friends were right! WTF is that crap!". Wind Waker was the reason I didn't buy a GameCube (that and Rare being sold). It was years later that I saw a friend play it and convinced me it was a great game after all, and now is my third favorite Zelda.... but at that time was a huge letdown.
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