Oh man, there was this bit in Skies of Arcadia....
That scene made me want to cry.
There was this giant whale that one of the supporting characters kept trying to hunt down throughout the game. Eventually, this character fell from your party. He reappered later with said whale, turning out to be a Gigas (a large, man-made creature that the old worlds sic'd on each other) that happened to be an actual whale.
Then they played the sad, music. The whale shed a tear and died.
Then they played the sad, music. The whale shed a tear and died.