My list is too long, lol.
Lots have been included already, like Balto, Kubo and the Two Strings, Iron Giant, Titan AE. Also, so many DC animated movies. Under the Red Hood, Flashpoint, Justice League: World War II, Gods and Monsters are all great. The Prince of Egypt is like the only religious movie I will willingly watch, lol. So much of the Ghibli catalogue, like When Marnie Was Here and The Tale of Princess Kaguya (still salty it got beaten by Big Hero 6 of all things. Oh, and the Secret of NIHM was so good too.