Link, it's called depression and it hurts all of us...
Arguably Nintendo's darkest hour, the annihilation of Clock Town in Majora's Mask has the audacity to go through with the apocalyptic horrors that most games hollowly threaten. From the gaunt panic of the citizens, to the final piledriving of the clock tower into the tumbling moon's forehead, it's a masterpiece in tragic chaos.
Any developer-fool can map out tearful checkpoints. It's far harder to give gamers the space to stumble upon euphoric jubilation. Pilotwings 64's hang-gliding photography tasks do just this. When you finally freeze that whale in a celluloid memory after hours of manipulating thermal pockets, all the swearing seems worth it.