My favorite is Majoras Mask. For one thing, it has a villain other than Ganon. Not that Ganon isn't a great villain, but he's over used, and Majora/Skull Kid is a refreshing change of pace from him. The main villain (majora)'s objective is somewhat original, not wanting to take over the world, but to have it be destroyed and metaphorically consumed by hatred and lust.
That brings us to the themes present in MM and the commentary on society and individual emotions that are thought provoking and in turn provoke emotion from the player. This mainly comes from the side quests, surprisingly, which were plentiful and fleshed out. The story lines were deeper and much more mature than anything found in Ocarina or Link to the Past. Themes like death, loyalty, sacrifice, love in the darkest of times, jealousy, resentment, longing for the brighter past, hopelessness, and many more were all over the place. These themes left you thinking and questioning your own life.
This is all supplemented by the music of Majoras Mask, which I believe actually has the best music in the series. The song of healing conveys the main theme of Majoras, which is healing. The music from the last hours of clock town really makes you feel like these are the last moments until everything you know is sucked into eternity, giving a sense of desperation.
All of that aside, the game is just fun. Once the player gets over the initial shock of the clock system it becomes quite enjoyable. There are only for dungeons, but they're more difficult than in OOT without being too frustrating like in ALTTP. The mask system was refreshing and added a fun new twist to game play. Seeing the characters from OOT return was nice as well because getting to see them in a new setting allowed them to be further developed.
Those and other reasons are why Majoras Mask is well deserving of the game of the decade award it received from Gamefaqs, and its place at the top of my list as the greatest Zelda game of all time.
