Probably, one of the most famous orphans in animation is Bruce Wayne (from 'B:TAS,' to 'B:TB &TB') even though Alfred is his legal guardian.
Kshin ('Defenders of the Earth') supposedly was an orphan when he lost his parents, and was taken and then abandoned by a yakuza-type gang on the streets, where he was the youngest member of a group of pickpockets until he was taken in by Mandrake the magician as his young ward, and later as his adopted son until his long lost Grandfather found him, their reunion was short though, after his Grandfather was killed saving Kshin's life.
Marshall John Bravestarr ('Bravestarr') is also an orphan, he never knew who his parents were, the only connection to his past was an heirloom medallion which was a mystery to him.
Tai Lung ('Kung-Fu Panda') another orphan, was found as a cub by Master Shifu at the door of his dojo. (in a flashback segment of the hit movie).