Well I just finished replaying OoT, and halfway through my first ever time of playing Majora's mask, gotta say I love them both, OoT for all the elements that everyone else has mentioned, it's outstanding story, gameplay, length, depth and it's sheer brilliance. However, to me it also has the Nostalgia factor, which in my opinion is a large contributor, because I used to play OoT ritualistically as a child, it was a rollercoaster of emotion for me, at times it frightened me, confused me, infatuated me (Malon

) and even frustrated me (When I was stuck as a kid, and then I'd spend forever in Kakariko playing my own games haha, like racing the workers or trying to jump of the tall post thingy) and whenever I think of OoT I feel at home.
Though it is unfair, because if I played MM as a child, I think there also would be a nostalgia factor but hey. And eventhough OoT is just the Deity of Video Games, MM does improve on some of OoT's shortcomings, though it is not as big as OoT, it certainly is much more dense: the story largely focuses on side quests and knowing characters in depth (Which I love) and it's more of an RPG, Graphics are nicer and also the fact that Link flips when he jumps never ceases to amaze me!

However, Majora's mask does get tedious, when you have to reset everything, I mean I have never been frustrated at Zelda games, even when I should have been because they're just so good that you can't stay mad at, but this factor was the first time I've felt something close to annoyance towards a Zelda game :/
TL;DR: Both solid games, could both easily be compared to "Mona Lisa's" of their kind, OoT is brilliant with a lot of things, MM expands on OoT, but OoT wins out on the Nostalgia factor!