Easiest way to answer would just be to list your top 3 favorite games ever, but some games are more defined by a few pivotal moments then others, so while Majora's Mask is my favorite game of all time I wouldn't put it top 3.
1. Ico : This game's last hour or so, starting at the bridge scene, is transcendent in it's gameplay-story integration. It changed the way I viewed video game storytelling, and left me in a dazed state just replaying "You Were There" and "Castle in the Mist" for a long time after beating it.
2. The Last Guardian : Replaying this fresh would be like reuniting with a best friend you never knew you had, only to lose them again. It would still hurt at the end when you have to part, but the incredible journey would make it all worth it.
3. Okami : For me while there's tons of enjoyable moments throughout this game, it is one that absolutely needed to nail it's ending to be a masterpiece, which it delivered on completely. The spiritball-esque cutscene during the final boss is my favorite cutscene in all of gaming, and it encapsulated everything that was endearing about the game up to that point. A rollercoaster of emotions ending on a howl of hope, as the sun goddess rises :