That's an extremely difficult question. No one Zelda game "kills" the others, they all have their strengths and weaknesses. Maybe my favorite is Ocarina of Time. I love the music, and it's pretty balanced in it's strengths. Good pacing, good dungeons, good sidequests and secrets. Majora's Mask is in a special place of it's own for being so unique. I really wanted to love Skyward Sword the most, because it had so much potential, but the game had some flaws. Still one of my favorites, though.
As far as the 2D games go, Link's Awakening is easily my favorite. I may like it as much as OOT, but it's hard to compare the 2D Zeldas to the 3D ones, plus it's a bit simpler than the console games.
Wind Waker gets an honorable mention for it's story, art, and setting.
...Can you tell I'm a Zelda fan?