I 100%I've yet to see an animated moment that had me choked as much as X-Men: TAS' "Graduation Day." Seriously, it's a RARITY for shows to have such a tearjerker finale.
I'm the only person I know wh tears up a little while watching Finding Nemo. I guess you could count that.
The best example that I can think of is the Beast Wars episode "Code Of Hero." Very dramatic how Dinobot took on all of the Predacons to save the early humans, and then sad seeing him meet his final fate at the end of the episode.
. If you're not emotionally moved by that, you must be some sort of robot.