I'm going to be perfectly honest here, so don't be hating on me or anything. As good a game as Majora's Mask was, there were far better games than it, such as (which I made a whole article about) Wind Waker, Half-Life 2, etc.
I mean, Majora's Mask did bring in some things that are used in games today, such as each character having it's own script and doing whatever they do at a certain time (which is echoed in Animal Crossing). On the N64, the game also looked quite good (Save the resolution. The one issue I have against N64 games is that they have beautiful textures and models, but it ends up getting killed by low resolutions of 320x240 instead of 640x480.), so that could be another upside.
As I said, though, it was a fun game with interesting characters that you could, in some cases, completely control their fate (besides the Moon). You could let some people have happy lives while others have a horrible time, which is something echoed in The Elder Scrolls: Oblivion and Fallout 3. So, great game, but certainly not the best of the decade (I could blame match-ups on that one. GameFAQs did have some horrible match-ups.).