Majora’s Mask. All day. Err day. I like it the most because reasons:

• Clock town is the most fully and beautifully characterized setting the series has ever seen.
• The transformation masks were just awesome. While other games in the series focus almost exclusively on finding weapons and equipment in dungeons, the masks added a new layer of depth that I don’t think any of the other games have matched gameplay-wise (see also: the shrinking in Minish Cap)
• It probably sported the most tangible reward for doing all of the sidequests in the game in the Fierce Deity mask. And to top it off, those sidequests were some of the most deep and involving in the series.
• The story is really good. And the atmosphere is just brilliant. It’s probably the darkest and most foreboding game on the N64 and in the rest of the series. I mean the whole goddamn game is about the impending doom of the world. Seriously the moon is falling out of the sky and if you look up you’ll see it crying about it. There is constantly a timer at the top of the screen telling you how much time you have until it hits. To top it off, all the good you do in any area is undone when you play the song of time to go back to the beginning of the first day when you’ve gotten what you needed. If you read deep enough into it (which you should) the game brings up questions about why Link is helping people. Is he doing it to be a hero? Is it because he genuinely wants to help people or because doing so will get him the things he needs? When it’s all said and done, are you really a hero after all? 
• Nintendo has more or less confirmed that it never really happened.
• Seriously play it it’s good.