Ocarina of Time wins my vote.

Although I enjoyed Majora's Mask immensely, the three day time limit and awful save system ruined it for me. Having said that, the music, environments and atmosphere of the game beat Ocarina of Time hands down. Unfortunately, the dungeons, while difficult, aren't exactly plentiful, whereas the dungeons in OoT are both challenging and numerous.

Plus, the Water Dungeon in MM is far more annoying than the Water Temple in OoT.