Way too many to name! I'll just jot down the first ones that come to mind.
Link's Awakening - The ending
Mother 3 - The first chapter, and the last chapter.
Dragon Quest XI - Several points, but most notably the mermaid story, Rab's side story, and most of the Dundrasil stuff.
Lufia 2 - The ending.
Final Fantasy X - I didn't like this game very much but it sure nailed the ending.
Final Fantasy III (SNES, six, whatever) - Triangle Island and the ending.
Skies of Arcadia - The ending. Geez, a lot of endings I guess.