That's a pretty difficult decision.
On the one hand, I feel like Ocarina of Time has to be a contender because it brought all of these beloved items - the hammer, the hookshot, the bow, etc. to the 3D world.
Then you have Majora's Mask, with all of it's utility masks, many of them allowing for different, very useful abilities, alongside many other classic items, plus two awesome swords: The Guilded sword and the Great Fairy sword.
Finally, you have Twilight Princess, which, as DekuNut pointed out, "We get two game-exclusive items in that one: the ball and chain and the spinner, both of which are super fun. Plus, we get the water bombs and stuff, which are useful, as well as two claw shots."
I'm not really sure that I can pick a favorite out of these three...