This is based on opinion. Please don't list it on a work's trope example list.
Tear Jerker / The Secret of Kells
Old Abbot Cellach in the Distant Finale. His spirit was broken after the Vikings broke through the defenses that he'd been working on for so long and hundreds, if not thousands people died because the wall was the only thing he concentrated on, rather then supports for the stairs to the safest building (which broke under the weight of so many people, dropping them to their deaths). Plus, he had locked Brendan, his own nephew and last surviving family member, in the scriptorium as punishment for working on something other than the wall. Said scriptorium was destroyed by the Vikings and Cellach was lead to believe for years that he had caused Brendan's death.
Cellach:"How can I rest, when our greatest treasure is gone?...He was only a boy..."
And the entire attack on the Abbey, as it results in the offscreen deaths of almost all townspeople and monks, which is overlaid by gorgeous choral music.
When Aisling seems to have been eaten/killed by Crom Cruach.
Aisling's Song. It is possibly the most beautiful song in an animated film, or in any film, period. The beauty is juxtaposed later on when the audience finds out Aisling does not get along well with Crom Cruach. Just listen to the words ... " ... you must go where I cannot ... " At least Crom Cruach was one of her own.