The ending of Pom Poko. Their attempts at driving off the housing development unsucessful, the surviving Tanuki who can transform do so and join the human world, leaving those who can't to a short life of scavenging. However, the public televised appeal some of Tanuki made to humanity at least kept the situation from becoming much worse. The final scene sees a small group of them singing and dancing joyfully on an empty golf-course, all that remains of their forest home. Even the song that plays over the credits is bittersweet.
Princess Mononoke: Ashitaka (permanently healed of The Corruption) and San fall in love, but they do not get together because San is unable to forgive other humans. Ashitaka promises to stay close enough to see San on a regular basis. Oh, and Irontown and the forest are both destroyed (though the forest is getting better...).
Despite Irontown being destroyed. The inhabitants decide to start anew, this time being closer to nature rather then opposing it.
Spirited Away: It's implied that Chihiro won't remember her adventures in the Spirit world, just like she didn't really remember Kohaku, or already thinks it was All Just a Dream. The English dub either leaves that part out or implies that she has kept the strength she gained over the course of her adventure. (There is a limit to how much bittersweetness Disney will tolerate.)
Even in the Japanese version, there's a possibility that her memories could be unlocked given the right stimulus, just as Haku's were when she told him his real name. This looks especially likely when you remember that Haku promised her that he'd look for her, and that the family appear to have lost several days if not weeks by the time they return to the car.
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).
Genesis of Aquarion: Apollo and Silvia finallyresolve their series-long bout of Will They or Won't They?... only for Apollo to then go and sacrifice himself to save the world. At least the promise of Reincarnation Romance gives it a more hopeful spin than other such endings...though it will take around 12000 years for that to happen, apparently.
Final Fantasy: The Spirits Within ends with the world saved, and the Phantoms at peace, but the entire cast save for two characters dead.
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.
Because at least one thing in the movie had to be historically accurate, Pocahontas didn't get to live happily ever after with John Smith.
In The Fox and the Hound, Todd and Copper manage to resolve a grievance fierce enough for the hound and his hunter guardian to trespass into a nature preserve to kill Todd. However, the two childhood friends will never be able to see each other again, but at least Todd has Vixey to console him.
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.
