My favorite of the series os Majora's Mask, bevause:
1. Majora's Mask has an interesting set of motives, and his childish attitude makes him a very enjoyable villain.
2. The graphics (As stated before) were ahead of their time.
3. The story and characters have emotional depth, giving you a reason to want to save everyone.
4. The soundtrack is the best in any Zelda game I've played yet, and with songs like Oath to Order and the Boss Battle theme, it truly was amazing.
5. The 3-Day system made the game challenging, but in a good way.
And that's what I think. Even if those Giants still creep me out.