To me, Ocarina of Time's storyline was simpler, but by the same token and in different ways...as dark as Majora's Mask. Majora's Mask looks darker because you get to SEE your demise happen if time's up and he premise of the moon; 3 Days. The time inbetween when you were a child and when you awaken as the Hero of Time seven years later, those times must have been hellacious as Ganondorf succeeded in conquering Hyrule, in Ocarina of Time. He wasn't just the dubbed King of Evil in that game. He was THE King of Hyrule and his influence spread far and wide and corrupted others, and others opposed him. Even Kakariko was plagued by fiends such as Bongo Bongo, and Volvagia within Death Mountain close by.
Ganondorf was just flat-out WICKED in Ocarina of Time, and I guarantee that if we got a chance to see everything that happened within the seven years that allowed Ganondorf to GET where he was during the era of the Hero of Time? Majora's Mask would have a tough opponent in Ocarina of Time for dark stories. The upside of both games, we get our happy ending after all, despite the odds thrown against Link.
Both fantastic games, but I'll have to go with Ocarina of Time here, for giving me my very first Zelda experience, and the King of Evil at his finest in an incredibly epic battle for the fate of Hyrule, nay...the world.