This is such a tough question. However, I voted for Majora's Mask. Why? I feel that Majora's Mask was a more character driven story than Ocarina was. You end up actually caring for the people in the Bomber's notebook, especially Anju and Kafei. Aside from this, cutting back on the epic feel of Ocarina (which is Ocarina's major strong point) is what makes Majora's Mask so endearing. The story is dark, and it constantly feels like you're discovering new things everywhere you go. It's like how The Empire Strikes Back is to the original Star Wars. New adventure with new characters and environments in a slower paced, more character driven world, with more danger.
But what sets Majora's Mask apart from Ocarina?
Simply the "Three Days Until Doom" game mechanic. You have to actually pay attention to time, and on top of that, if you wish to finish certain sub-quests, you have to learn everyone's schedules. This also affects the emotional feel of the game in that every time you play the Song of Time to go back to day 1, you can't help but feel a little sad for everyone you just helped...again, I go back to the Anju and Kafei quest. To me that was the most emotional moment in the whole game when you finish the quest with less than an hour and a half left until the moon crashes. I almost didn't want to play the Song of Time because I knew as soon as I back at day 1 they'd be back to where they were before I brought them together. Not to mention they just get back together as the Moon is about to collide with Clock Town. Anyways...Majora's Mask gets my vote, it's dark, emotional, and just a great game.