I don't know if I could pick an overall favourite, many of them are quite different from each other. But I could narrow down the choices. For 3D, it'd be Ocarina of Time. Maybe it's just because it was the first, but I still feel the game has the best balance of gameplay and pacing. I didn't like Majora's Mask because of its poor structure, Wind Waker wasn't meaty enough, and Twilight Princess... well, it was good, and if I played it first, I might prefer it over OoT. So my 3D pick is pretty easy to make.
For 2D though, it's tough. Sure, Link to the Past was really good for all its refinements. It is also really easy. The NES original has its charm for being the most difficult of the bunch, and I seem to be an oddity for liking Zelda II. I just can't decide between the three because they each have their strengths and weaknesses. The Game Boy ones are okay, Link's Awakening is the best of those, but... I don't know. They didn't really click with me. Although I haven't played the GBA one yet, or the DS ones (I'm not sure if those count as 2D or 3D).