Ocarina of Time. I've only gotten halfway through Majora's, but I'm planning on finishing it up within the next few weeks. Either way, I think the dungeons are much better in OoT. The first two in MM aren't really anything to write home about. I know the Stone Tower temple is supposed to be amazing, but one amazing dungeon does not outweigh all the amazing ones in OoT. I particularly love the Fire and Forest Temples. As well, I'm not a huge fan of the 3 day thing, and the intro for MM goes way too long. The fact that you can't save until you get back the Ocarina is kind of annoying. I've also never been a fan of having to constantly switch "personas" in games, like you do with the masks in MM.
I still like the game, but I like OoT way more.