Pinocchio: The main protagonist gets reunited with Geppetto and becomes a real boy, but most of the villains, specially the Coachman, are never punished. And those hundreds of innocent children who were taken from their families, turned into donkeys, and sold into slavery? They're still donkeys and no one comes to save them.
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.
Melody Time: Happens in two segments. Johnny Appleseed dies, but has left a huge legacy in his wake and is off to grow apple trees in heaven; while Pecos Bill gives up being a cowboy after the death of his fiancé Slue-Foot Sue, but Texas is implied to be a much safer place because of him.
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 to the farm as the foxes watch him from afar.
Pocahontas ends with 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.
They eventually do see each other again in the direct-to-video sequel. John Smith is well. But by that point, Pocahontas has fallen in love with someone else.
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.
Toy Story 3: The toys now have a new owner, but they have lost many of their friends to yard sales, donations, and breaking, and will probably never see Andy again.
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 the first three in the process of freeing the town from the evil tyrant; however the girl, while clearly caring about him as a friend, falls in love with a Knight in Shining Armor. Jack turns back into a spirit and blows one of his wintery gusts through their wedding, and the girl comments that it feels like "an old friend kiss[ing] the bride."
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, aside from a brief, chance reunion in her wolf form, it's quite likely Aisling and Brendan will never see each other again.
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, knowing he and the titular princess will never be together, and flies away. But not wanting to be without him, the princess begged her father the king and her nanny to turn her into an egret, knowing she won't ever become human again, and possibly not see them or her friends and subjects again. The movie ends with the two birds flying together (and helping lost ships) as the credits roll, accompanied by this song.
In Monsters University, Mike and Sulley are expelled from the university but they become the close friends that they were in the first movie. Also, they work their way up from being mailmen in Monsters Inc. to eventually become a scarer and assistant team, fulfilling their dream. Mike surrenders his life-long dream of becoming a Scarer and settles for being a Scare assistant. It's a lower position than what he aimed for, but he feels like an equal as he is the one in charge of coming up scare tactics.
In Jack and the Cuckoo-Clock Heart, it's implied that Jack dies as he's finally kissing Miss Acacia, considering he's in bad shape and he threw away the key that keeps his mechanical heart running. Romance is dangerous for Jack's heart even at the best of times.
At the end of Corpse Bride, Emily breaks off her engagement to Victor, allowing him to return to his real fiancée. Even though she doesn't get to marry him, her soul is finally free to move on, and she ascends to the heavens in a flurry of blue butterflies.
At the end of The Fantastic Adventures of Unico the evil baron is killed, Katy has found a new home, everyone is happy... but then the West Wind returns and Unico must leave and forget his friends forever.
World Of Tomorrow: The young Emily safely returns to her own time period, but the cloned Emily is left to die in sixty days due to a meteor, not to mention that young Emily will eventually grow up into her cloned self.