The ending of the second half of Pikmin 2. As the spaceship flies off into the sunset, Olimar sees a light dot the ground below, followed by another one, and then another one, until the whole land is filled with sparkling lights. The source of the lights? The Pikmin, who are glowing as they watch Olimar depart. It's their way of saying good-bye and thanking him for helping their species survive.
Not sure if fan animations count, but this video is just... Well, it just needs to be seen.
After finding Gyromite Blocks in dungeons as treasures throughout the second game, what is the name of the treasure that is ROB's head? Remembered Old Buddy. Awww.
That may be quite a stretch, but the fact that the Sagittarius and the Libra are considered mandatory parts is heartwarming: these parts serve no purpose to the Dolphin, as the ship can fly perfectly fine without them. However, they are souvenirs given to Olimar by his children, and as such are considered mandatory, meaning, in a way, that Olimar would rather die than leave behind a gift from his kids. Awwww...