All the endings of Fate/stay night that aren't outright downers are bittersweet, because just as Shirou's father warned him, he can't save everyone. In particular, either Saber or Ilya has to die, and in the only route where Sakura isn't left in the hands of her (horrifically) abusivegrandfather (who might kill her), the only non-downer ending has both of them dying. The first route (which is the one followed by the anime) is the most bittersweet: Shirou wins the war, destroys the Grail, and avenges his father, but Saber is gone, and nothing can take her place in his heart. We're left to ponder what "continuation of the dream" Saber might be seeing, and to hope it'll bring them back together somehow.
In the True Ending for Arcueid's route, Arcueid technically survives, but after saying one last goodbye to Shiki, she leaves to sleep, presumably forever now that Roa is Deader Than Dead. However, the manga ending has him track her down and they reunite, perhaps to keep it consistent with sequels.
Arcueid's is easily matched, bordering into Downer Ending, by the True Ending for Hisui's route, with Akiha killed by SHIKI, Kohaku committing suicide, and Shiki and Hisui leaving the mansion.
Likewise, both of Akiha's "good" endings are bittersweet. In one, Shiki saves Akiha's life by seeminglynote Kagetsu Tohya has a sidestory that continues from this ending which confirms that he lived killing himself so that the lifeforce she lent him will return to her. In the other, Shiki can't kill himself, so Akiha lives out her life as an insane beast that feeds on his blood.
Ciel's good ending is unambiguously happy, on the other hand, unless you're Ciel herself. Why? Because Arcueid cheerfully sticks around and decides to go for a threesome ending of sorts. Ciel is not happy about having to share in her good end. Shiki himself also spends much of his time figuring out how to keep Arcueid and Ciel from killing each other.
In the freeware Visual NovelNarcissu, emotionlessIll Girl Setsumi escapes her bleak existence of hospitalizations and discharges, experiences life on the open road, and finds a little bit of happiness for the first time- then promptly kills herself. It's implied that the unnamed protagonist (also ill) doesn't last much longer.
After sitting through the credits for G-Senjou no Maou, you are treated to a Mood Whiplash epilogue. After surviving the chaotic incident he instigated in the climax, "Maou" pays Kyousuke and Haru a visit, which culminated in Haru chasing him and attempting to gun him down. Kyousuke intervened by killing Maou with his own gun, sparing Haru from the media attention and thus, protecting her future as a violinist. After spending 8 years in prison, he meets Haru and her daughter, and assumed that she got together with another person. The trope is then subverted when he asks how old the girl is, to which she replied:
I'm seven years old, daddy.
Steins;Gate true ending, ends with Rintaro preventing both the bad future and Kurisu's death, but the Lab member except Rintaro doesn't remember any of their experience together and Suzuha disappeared because of the Time Paradox created by the new timeline and there's a chance she might not exist in this timeline. But it is hinted that the members might not have completely forgotten their memories, as shown when Rintaro met Kurisu again in Akihabara and she still has memories of the nicknames Rintaro gave to her
Kara no Shoujo's best endings are bittersweet at best. Yes, Reiji lives and the murders stop but most of the cast is dead including (normally) Toko. And the ending she lives in is a downer ending. The ones that are bittersweet instead of downers are the ones where he catches Rokushiki and is impied to start a relationship with either Kyoko or Hatsune.
Depending on which side of the fantasy fence you sit on for the possible endings of Umineko: When They Cry, the final fate of all the cast members is either this, where the Metaworld is real and Battler is reunited in death there with Beatrice and his whole family or a downer, where the whole thing is just made up as a way for an amnesiac Battler to sort out his own thoughts about the Rokkenjima incident. Still, no matter which viewpoint you take, it doesn't change the fact that by the end of the series, almost everyone who was on Rokkenjima is dead.
Sampaguita: Don't expect coming out unscathed of saving Maria from the Yakuza's clutches by storming their headquarters with Boy and pals, as there's only two possible outcomes: either being jailed for gunning down the Yakuza boss who was trying to shoot Maria; or being killed by said Yakuza boss by protecting Maria with your body. However, after those events, you'll discover (either after you've served your 5-years jail time and reunited with Maria in her native Philippines, or after awakening as a ghost 2 years after your death), to your joy, that Maria had become pregnant with your kid during the time you were living together, and gave birth to a little boy.
Hanako's "Friend" ending results in Hisao and Hanako sharing a simple dinner and a nice chess game... but never developing their relationship past mutual friendship. It's also implied that this sort of relationship will eventually prove self-destructive, since Hisao will put Hanako's needs ahead of his own.
Shizune's Good Ending can be interpreted as this. It has Shizune, Misha and Hisao preparing to go their separate ways on the eve of graduation while vowing to remain friends and to see each other again one day. They even take a picture doing the Musketeer pose at the gates. It's not explicitly said that they're forced to completely separate, though, and it's said in the game that it could really go in any direction.
Lilly's bad ending can also be interpreted as this. Hanako has finally come out of her shell and is making friends on her own, Hisao has found a new direction in his life and a good future ahead of him, but the woman he loves leaves forever for Scotland, to live with her family who she barely even knows, likely spending the rest of her days unhappy, ending up as Star-Crossed Lovers.
Yandere Chan: The only good ending in the whole game is this. Mia's mental instability is discovered and she's being treated, no one died in the process, and the main character still loves her. However, it's noted that Mia will probably never be healthy enough to leave the mental asylum, and the main character seems to be putting their life on hold just to be with her. The rest of the endings result in your bloody demise.
Dangan Ronpa has one: The good ending features the six surviving students escaping, only to find the outside world ravaged by the Despairing Incident.
999: Nine Hours, Nine Persons, Nine Doors, the True Ending (which, admittedly, is the only one that isn't an outright Bad Ending). Yes, the only death among the "nine persons" is the one who dies before the very first dialogue choice, but Junpei never gets to see Akane again, chasing after her for the rest of his life.
All of the endings in the Coda section of White Album 2. Even Setsuna's True End, the closest thing in the game that could be considered a traditional Happily Ever After ending, still hints that not all things are right behind the scenes.