I have to split my vote between 2D and 3D. They are similar but don't really fit the same niche in my eye. 2D usually has much better Puzzles and 3D is far more Cinematic.

2D: Oracle of Ages/Seasons. These are the quintessential 2D Zelda game/s in my eyes. I prefer Ages over Seasons but really they are two parts of the same Story so I count them as one.

3D: Ocarina still has my vote. Sure it is smaller than by today's standards, but size alone doesn't make a game. Ocarina is full of loveable Characters, phenomenal Music, fantastic Dungeons, and one of the best Stories in a Zelda game. Not only that, but it is perfect as an introductory into the series, much more than any other Zelda in my opinion.