The new Zelda U should feature multiple endings.

[2Quick]

Well I sort of consider Majora's Mask to have multiple endings... depending on how you look at it...

It has different epilogues depending what side quests you finish.

plus, depending on how much you read into the game, you could view beating the game with/without using the fierce deity mask as alternate endings. There are intense theories online speculating about why Majora would let you have the ultimate weapon against him (the fierce deity mask). Is he just tricking you into thinking you defeated him? what dark force is controlling you as you put on the mask to beat him? Is he proving a point by forcing you to succomb to the mask to beat him? Is he just trying to cause more chaos? If you beat majora without using the mask you know you have bested him, and there is no potential risk of being tricked/ succumbing to a darker force yourself.

^^
This is all a bit too speculative for me personally, but its interesting to think about. And it makes me feel cool for beating it without the mask.