Hmmm, well before I can answer the question, you have to consider both of the games.
Ocarina of Time was Zelda's very first 3D game. That already gave fans something to be excited, but with an interesting storyline, people were easily sucked in. I found the story to be very good, and really original. Although it did the usual "Princess got kidnapped, go save her" concept, there was more than just saving Zelda - like in most Zelda games. However, there were so fun side-quests, good dungeons, and interesting characters. In its time, it was a tough game to be better than, even now it's tough to top this game's beauty.
Majora's Mask was the follow-up to Ocarina of Time but with a darker turn. Basically it was a race against the clock, not just good versus evil. This time, you weren't saving a Princess; you were saving an entire land. It consisted of four dungeons that increased in difficulty as you continued - it's a weird thing to point out, but I've found dungeons before another to be harder. It contained many sidequests, and many amazing characters. As you progressed through the game, you felt more and more connected to them, whether you were letting a man see his chickens grow up, or helping a little girl fend off aliens. This game - unlike Ocarina of Time - definitely revolved around sidequests and less upon the actual main story.
Now, to compare the two games. I found Ocarina of Time to have much better dungeons and puzzles, but Majora's Mask's overall story definitely won my favor. The sidequests were more in-depth in Majora's Mask, and at times more rewarding. And there were many of these great sidequests in Majora's Mask, unlike Ocarina of Time. In Ocarina of Time I found the characters to be very cookie-cutter, but Majora's Mask offered more. From the eccentric and mysterious Happy Mask Salesman to the remorseful Guru Guru, you felt as if you knew these characters. I enjoyed Ocarina of Time's weapons better than Majora's Mask, especially the different swords.
So overall, I have to say that I liked Majora's Mask just a little bit better than Ocarina of Time.