Squeaks turning into a butterfly at the end, and Dinky and Boomer deciding to let him go. Also very symbolic of the larger plot where the hunters and prey reconcile.
During the fight with the bear when Amos Slade realizes just how outmatched Copper is and that all he can hope to do is aggravate and distract the bear, he abandons his attempts to escape the trap and instead tries to reach his gun. While subtle, it sort of highlights just how much he cares for Copper.
Copper and Chief's bonding.
Copper tracks down and mercilessly hunts Tod and his mate, looking like he won't hesitate for a second to kill him should he get a hold of him, yet when Tod witnesses Copper about to be killed by a bear, he simply can't let it happen and rushes in to save his former best friend. The look of absolute amazement on Copper's face right as he stares at the exhausted fox who had just saved him despite everything that had happened really sells it.
Pretty much every interaction between Copper and Tod when they were young is completely adorable. Unfortunately that just makes it all the more tragic when they have to go their separate ways.