I'm not surprised at all by Metroid Prime getting the most votes, but Zelda: Majora's Mask? I guess I just don't get what makes that game so great, I felt it was kind of substandard and forced.
Majora's Mask was designed around a short development cycle, many of the "innovations" were most likely out of necessity to get it out the door on time. To me MM feels like the most non organic Zelda in the series, and LOOKS designed.
This is an interesting criticism of MM. I think that it has possibly created the most organic world in any game that I've played. There are something like 25 people that you can help in your bombers notebook and each person has there own schedule that they follow with windows of opportunity for you to help. There are only four dungeons but before each dungeon there is a task that must be completed in the dungeons respective town that is like its own dungeon. This is the most organic integration of dungeon like problem solving in any zelda game, better than the yeti's house in TP and better than the well where you get the eye of truth in OoT. Each mask comes with a story and has a function, not to mention that you get a different reaction out of everyone you talk to.
I also think that the locals are much better than in OoT. They are much more specialized and intricate. Clocktown is bigger and more intricate than Hyrule Castle town and Kakariko village put together, the swamp is detailed and introduces the deku scrubs as serious third race, the Gorons are more developed than in death mountain. I always liked Zora's domain better than the Great bay though.
I think that the time limit throws people, and that a lot of people got put off early and didn't really give the game a chance. The game really gets more and more awesome the further into it you play. One thing that I really liked was that right from the start of this game link was a badass. He doesn't have the master sword, and it's not even clear that he has the tri-force of courage, but he has this composure from his previous adventure that stands out to me.