The ending of mystery dungeon sky (not mystery dungeon blue so much, I WANTED to return safely to the human world, the alternate pokemon world being rife with danger and all). After all this time (over 10 years of me liking the franchise), pokemon finally got me to shed a tear, but that was mainly because it caught me by surprise of how emotional it was.
On the other side, Ash's death and revival in the first movie to me was extremely narmy - even as a child, I thought ash being cried to life was a pretty stupid deus ex machina