Make Mine Music: In the final segment Willie the Whale is harpooned, but now he's in heaven, free to sing to his heart's content.
The Fox and the Hound: After Tod and Vixey narrowly escape death at the hands of Amos Slade and Tod's former best friend Copper, Copper and Slade are attacked by a huge bear. Tod saves Copper's life but is injured in the process, leaving him at Slade's mercy, who in the end decides not to kill Tod after Copper induces Slade's Heel Realization. Tod and Copper depart with tiny smiles at each other and Copper returns to his life as a hunting dog. Tod and Vixey watch him from afar, with audio clips of young Tod and Copper being played over the scene as the movie ends.
Pocahontas: The conflict between the Powhatan tribe and British settlers has died down. Chief Powhatan has accepted his daughter's love for an outsider. The British settlers come to see that Governor Ratcliffe was the only one really in the wrong. But also, John Smith was shot trying to protect Chief Powhatan from Ratcliffe, forcing him to return to England and leave Pocahontas behind. The lovers wave goodbye to each other with the strong possibility they may never see each other again.
Sky Blue. Sure, Ecoban falls, but Jay will almost certainly die, and Woody isn't in great shape either. Oh, and they were wrong about Gibraltar.
Once Upon a Forest: The Furlings manage to make it back in time to save Michelle, some humans clean away the remaining poison, the inhabitants of Dapplewood come back and the Furlings are reunited with their families. However, the plantlife of Dapplewood is still damaged , and some of the animals had been killed by the poisonous gas (including Michelle's parents).
Also consider the Epileptic Trees regarding the fate of Aki's child, whose life may or may not have been forfeit in order to create the Eighth Spirit.
9 ends with The Fabrication Machine finally being destroyed, and 1, 2, 5, 6, and 8's souls being released from the Talisman, so they're finally at peace. But the world is still badly messed up, and the remaining Stitchpunks aren't sure what's left. And the microbe-like creatures in the rain imply that they might've somehow restored life. Probably.
The old Rankin/Bass christmas special Jack Frost. It's about the titular magic spirit trying to become human because he fell in love with a girl. But to be human he needs a horse, a home, gold, and a wife. He manages to find all of those in the process of freeing the town from the evil tyrant, but couldn't get the girl to fall in love with him, and she ends up marrying someone else. It ends with him simply returning to the heavens and abandoning becoming a human.
In The Secret of Kells, the wall did not manage to keep the Vikings out, and there were numerous casualties. Brendan, Pangur, and Brother Aidan managed to escape the carnage and the Book of Kells was finished years later, but during this time Brother Aidan died of old age, and the Abbot believed Brendan was dead for several years. He and Brendan are finally reunited in the last scene of the movie, however, but despite the fact that Aisling may or may not be able to return to her human form, it's quite likely she and Brendan will never see each other again.
...Except that she did turn into her human form when Brenden returned.
In The Last Unicorn, the last unicorn (Amalthea) finds and frees her fellows, but at a price. As a human, the Lady Amalthea falls in love with Prince Lír. Returned to her immortal form, she can no longer stay with him (or even feel love anymore), so she leaves both her love and her two human friends behind to return to her home in the lilac wood. Even sadder, however, because she has experienced love, aging, and regret—experiences foreign to "pure" unicorns—she is no longer as innocent and aloof as others of her kind, separating her even from her own species. And yet, as sad as these things may be, she thanks Schmendrick for them. It is a good thing to have known love.
In The Admiral and the Princess (aka The Blood Crystal), the Big BadCourt Mage has been defeated after his amulet (the Blood Crystal) has been shattered (killing him). But unfortunately, the titular admiral forever remains a heron, and the Big Bad's amulet was the only thing that could turn him back human. The admiral realizes this, and flies away. But not wanting to be without him, the titular princess begged her father the king and her nanny to turn her into a egret, knowing she won't ever become human again, and possibly not see them again. The movie ends with the two birds flying together as the credits roll, accompanied by this song.