In Wind Waker, Link using the Triforce of Courage to open the way to Hyrule in Wind Waker, and then finding that said Triforce of Courage has come to dwell within him: the rendition of the Zelda Main Theme that plays at this moment always gives me goosebumps.
In A Link Between Worlds, the entire ending never fails to get me misty-eyed.
In Minish Cap... every time Vaati is on screen. Story-wise, he's an incredibly clever and menacing villain-- to the point where if you take too long to get through Dark Hyrule Castle, you get a non-standard game over because Vaati manages to completely extract the Light Force from Zelda, which kills her. Nice job, hero.
And of course, who can forget that classic line from Breath of the Wild-- "But courage need not be remembered... For it is never forgotten."