Ace Combat: The Equestrian War ends with ponies winning the war and reconciling with the griffins. Unfortunately, many ponies and griffins died during the war, many were traumatized and majority of Equestria was ravaged by the conflict. However, the epilogue goes toward Earn Your Happy Ending for some characters.
For the most part, the ending is far more sweet than bitter: The Seraphim and his Religion of Evil are defeated, Stephanie's surgery on her ACL is successful, Cassandra successfully converts to Catholicism and even has a love interest. The bitterness comes with the fact that her love interest is another woman. While their relationship is just sweet and fun now, if Cassie continues persuing same-sex relationships into adulthood (with her current girlfriend or anyone else), she will almost certainly face scrutiny and ostrization from the religion she is now so dedicated to.
A second epilogue (that the author himself isn't sure is canon) is still bittersweet, but more hopeful. Three years after the events of the fic, Cassie asks her girlfriend Sadie to marry her. She has accepted the Catholic Church may ostricize her, but they can never take away her relationship with God and Christ. She also states that when (not if, when) the church realize the error of its ways, she will forgive it.
Children of an Elder God: At the end, Shinji and Asuka have lost almost everyone that they care about, and due to their mutations they don't fit into human society any longer, so they abandon civilization forever. Still they are still together, the narration states that their remaining friends will meet them again, and thanks to them humanity has been saved and will endure for several centuries more.
Clash of the Elements: The end of Part 1. Though Alex has become the Elemental Overlord and stopped Joe Dark, the Genesis Samurais are dead and the Inner Guardians' spirits will never be given the freedom Alex wanted to let them have after taking their souls into their bodies. Not to mention that because of the Star Spirit's interference during the battle Geno has to stay in Star Haven to mediate the world below. That's not even getting into the fact that Cackletta is still alive and so are Dimentio and Smithy.
The My Little Pony: Friendship Is Magic fanfic, The Conversion Bureau: Not Alone ends on this note. After getting soundly defeated by humanity's military forces trying to stop her conversion crusade and sustaining heavy casualties, Celestia takes Equestria and they retreat back to their own home dimension, but in the process, are forced to leave behind about three thousand ponies. The good news is that Equestria won't be bothering anyone else anytime soon, humanity of course survives, there is hope for peaceful coexistence between humanity and the ponies that were left behind on Earth, and the last chapter has the Queen of the Gryphons state that Celestia will have to answer for her crimes eventually. The bad news is that the PER and HLF are still out there causing trouble, hundreds of ponies are still stuck in the internment camps despite the growing international pressure calling for their release, South Africa is rapidly turning into a fascist hellhole, and several countries start spending large amounts of money (at the cost of education and healthcare) beefing up the military for a war that will never happen.
Dirty Sympathy ends with one. Klavier and Apollo can never return to U.S. without being sent to jail by Phoenix and both of them lost their careers. Apollo and Trucy never find out they're blood-related and will never see each other again. Phoenix's plans of restoring the Jurist system might be for naught as Kristoph's rightful convinction is dependent on a crime he didn't commit. Edgeworth decides not to rekindle his relationship with Phoenix, seeing the price for it too high and will lead to inevitable disappointment. But Klavier and Apollo are free of their tormentors and are given a second chance at life. Klavier and Apollo are happily in love with each other and won't be sent to prison. Phoenix gets his reputation back and can start using his connections to start doing major good and Edgeworth gains two apprentices to help him.
In the My Teen Romantic Comedy SNAFU fanfic The End of the Affair, Hachiman and Yukino have met up and more or less reached a resolution of their mutual attraction from high school. Unfortunately said resolution is basically them reaffirming how they would never get together due to the consequences of their choices and following their ideals, ending with them going to live their separate, and quite possibly unhappy, lives once more with the implication that they would never see each other again.
The End of Endsends with Terra returning to being a Titan, the universe being saved from the destructive powers of the Dark Prognosticus, and Count Logan finally coming to his senses and redeeming himself. However, his injuries got too much for him and he died, which caused the Titans to feel bummed because Count Logan was really Beast Boy.
Fallen King ends like this. Pegasus was stopped from getting the Millennium Puzzle, both Ryou and Yami Bakura are presumed dead, and Joey, Tea, and Tristan have escaped with the soulless Mokuba. However, Joey realizes that they'll never stop being hunted, declares that they cannot be friends, and the trio separate to save the world.
In the MLP fanfic Falling Backwards, after Rainbow Dash suffered sever brain trauma, that reduces her to having the mind of a small child, it seems like a hopeless situation, until the Princesses come up with a solution. The catch? It involves physically regressing her to her current mental age. Which will give her a new lease on life, but take away the chance of her friends ever getting Rainbow back in their generation and making it improbabal that she will ever be exactly the same again.
The Friend has two bittersweet endings and one that is a complete downer.
Ending A has Star Wolf being defeated by the protagonist and the Star Fox team, however, thanks to Corneria's corrupt police force, Fox and Peppy are shot dead right in front of the protagonist and Falco is struck by an EMP blast, bringing his Arwing down to the ground and supposedly dying on the crash. Then, the protagonist is arrested...if not killed.
Ending S has the protagonist killing himself to avoid doing what Star Wolf demanded him to do. With the protagonist's dead, Fox McCloud is struck violently by it and enters deep depression, never understanding why his best friend did that.
In the Axis Powers Hetalia doujinshi called "From the New World with Love", England wakes up from his coma and America is redeemed, but... America is very much Lonely at the Top and knows that one day, the monster that was unleashed in WWII will come out again. There's a reason why it has two sequels, a "good end" ("Miracle of a Superhero") and a "bad end" ("Tragedy of a Superhero")...
Ghosts of Evangelion: The story ends in 2080 when Asuka passes away and Shinji dies three days later. However they have a daughter, grandchildren and great-grandchildren, Kaworu and Rei visit Shinji when he dies and Rei hints that he and Asuka will be together in the Afterlife. After their death Ryuko, Kyoko and Misato go about their many accomplishments when they were alive.
HERZ: After the last battle Shinji and Asuka are alive –and expecting!-. Most of canon characters have survived, Yui and Kyoko’s souls have been released and SEELE has been defeated once and for all. However Rei seals herself together with the Evas, Adam, Lilith and the Lance to ensure that they will never be used again, which means she has to say goodbye to her family forever.
The Girls' Generation/Super Junior crossover fanfic Kill Or Be Killed. Sunny is the SNSD winner and Yesung is the SJ winner, and they are both taken away by their group managers, leading them to outcry in anger after realizing that all of the story's events could've been prevented had they interfered, especially with Sunny in a state of distress after her lover Sungmin is killed. Ryeowook is stabbed by Sunny and left for dead until Sooyoung (who he thought he had killed) nurses him back to health and asks Yesung to look after him while she goes in pursuit of a new life. Additionally, Jessica survives by escaping the amusement park Shawshank style.
In the Total Drama story, Legacy, which is set ten years after the events of the show, Heather and Duncan spend much of the story reminiscing about the death of a colleague, a tragedy that disrupted the season and nearly killed the show. The late colleague was someone whom Heather couldn't stand whilst they were living at the camp; but ten years later, the more mature Heather reveals a heartfelt gesture of remembrance to her late enemy.
In Marie D. Suesse And The Mystery New Pirate Age!, the Disinfector manages to, with the help of the Suesse family, push the Reset Button and undo 20 years worth of terrible events in the One Piece universe that include the deaths of Luffy and the rest of the Straw Hats, but one of the events undone in the process is Madelyn meeting Garreth and having Mar with him. However, the last scene shows Garreth and Madelyn meeting again.
The Dashverse story May the Best Friends Win ends with Trixie admitting to being a Jerkass and apologizing to everyone, thus saving her and Rainbow Dash's friendship. However, she can't bring herself to stay in town, saying that she needs to leave and make her own friends, rather than leech off of Rainbow Dash's life anymore.
In Naruto:Asunder we have the Akatsuki defeated, Minato and Kushina are still alive and the five elemental nations are at peace. The cost however was Gaara, Tsunade, Jiraiya, Kankuro, Lee, Hinata (who's dying words were "Naruto-kun. You still owe me a date.) and Naruto. They do become legends though.
In ''Necessary To Win, Oarai wins the tournament, enabling it to stay open. Several other characters have accomplished what they have set out to do; Miho has found her own way of tankery, Saki and her sister have reconciled, Nodoka is allowed to stay a her current school, Mako gets the tardies stricken from her record, and Hana has gotten her mother to accept her doing tankery. Not all characters are satisfied, though; Saki and Teru's parents divorce, rather than getting back together as they had hoped, and in the end, many characters, such as Momo and Yumi, are forced to say goodbye to each other as a result of graduating. Some problems remain, as Miho's mother has not disowned her, but does not regret doing so, and the future of Oarai is by no means guaranteed. But the characters remain hopeful, and remain committed to working toward their goals, with Miho and Saki having come to enjoy tankery again.
At the end of Neon Genesis Evangelion: Genocide, SEELE still exists, NERV’s workers are at the mercy of the Japanese Government, and Shinji and his family lose their home. However, Instrumentality has been averted, Keel has been assassinated, leaving SEELE without a leader and at the risk of being exposed, and the main characters are safe and sound.
A New Chance For Adventure: At the end of Hunting The Hunter, Ash and his team succeed in defeating Rico and saving Team Rocket's Pokemon, with the covert help of Skailyn, but they arrive too late to stop him from selling Larvitar's mother to Team Magma, and have no leads with which to find her. Not to mention Latios giving into his anger and offing Rico behind Ash's back.
The first work of the Ouroboros series, Wake The Storm, ends with Anakin swearing to never turn to the dark side and reuniting with Obi-Wan and Padme after they thought he was captured and brainwashed by Seperatists and Anakin killing Palpatine. However, as he's dying, Palpatine executes Command Code Retribution, resulting in the Jedi, planetary leaders, CIS leaders, and the Senate all being killed and the armies of the Republic and Seperatists going rogue.
In Perfection Is Overrated, the SUEs, the Usurper, and the Obsidian Lord and his minions are defeated. Not everyone survives, though- Hitomi killed over 20 innocent people and Yukariko died thwarting Ishigami's plan- and unlike in canon, their deaths were not undone. The surviving Himes have various problems to deal with in their lives, both mundane and magical (Shizuru, despite Natsuki having accepted her love, must one day deal with how her parents will react to her coming out of the closet), but they resolve to face those problems in the future (Nao, for example, overcomes her bitterness and hopes to become someone her mother can be proud of when and if she comes out of her coma), having realized that this world and their lives will never be perfect and chosen to face those challenges.
The the alternate ending to the Kill la Kill fic Piano Notes is this. Despite everything, treatments, surgeries, and all, Satsuki's illness still takes her life, however, as on her deathbed, she tells Ryuuko how much she's made her happy and that she loved her.
An earlier fic by the same authoress titled Sunshine (sequel to Raindrops, which has a Downer Ending) has a terminally ill Satsuki being Peaceful in Death and being reunited with her sister, Ryuuko.
In A Pikachu in Love, after spending the entire fic questioning his relationship with Ash and growing closer to Pichi, Pikachu finally realizes just how much Ash and Co. care about him, and decides that it's too important to ever doubt or break. Unfortunately, on the same night he plan to tell Pichi that it would be the last time he would see her, Pichi had already realized she was in love with Pikachu and plan to tell him that on the same night. Though she manages to tell Pikachu first, and Pikachu does admit that he loves her to, he was forced to explain how he can't leave Ash just like that. Though hurt, Pichi understands, and bids a tearful goodbye to her love for the final time. What keeps this from being a complete downer ending though is that Misty, who had secretly followed Pikachu and saw it all, managed to get the jist of what's going on and quickly comforts Pikachu, reminding her how much she, Ash, and Brock all love him. On top of that, there's also an implied chance at the end that Pikachu will see Pichi again someday.
The small group of friends journied on under the bluest of skies, the most golden of sunshine, and Pikachu took pleasure in smelling the clean air that gently blew into their faces. It felt like the world was beautiful all over again, and that there was something special waiting for him at the end of the road…
In Pipeline, Ben's okay, Ace establishes that he's a good father, the Utoniums are slowly accepting Buttercup's death, and Kevin and Dexter have agreed to be civil for Ben's sake. But... Ben and Kevin still need to work some things out, Kevin's betrayed Gwen's trust by keeping things from her, Buttercup and Mac are dead, Kevin and Dexter will never really be friends, and the war still isn't over. Ouch.
The Dark World of the Pony POV Series ends like this. The heroes finally earn their happy ending by overthrowing Discord and defeating Nightmare Paradox, restoring harmony to the world and even managing to resurrect everyone killed by Discord or his minions during his reign of chaos. However, those who died indirectly or through old age (like Pinkie Pie and Fluttershy) remain dead, and there's also the fact that Twilight has become the Alicorn of Happy Endings, and now has to leave to help other worlds reach their happy endings as well, leaving her friends behind to their well deserved happiness.
The Pony POV Series Chaos Verse: The Big BadNightmare Phobia is destroyed, and Discord and Fluttercruel make peace with the Princesses, but the Construct Ponies are all dead, leaving Discord and Fluttercruel alone in Limbo once again. Though the Constructs also managed to gain their own souls and earn a place in Pony Heaven and Fluttercruel manages to reconcile with Fluttershy with Luna's help. The last scene has Discord begin recreating Chaos, with Celestia offering her and Luna's help.
The Predespair Kids ends like this. During the finale arc, Hope's Peak Academy is invaded by an army of Monokumas, Ibuki, Kazuichi, and Chihiro are all revealed to have fallen into despair, Ryouko learns that she's a clone of Junko before Yasuke mercy kills her to spare her from a worse fate at Junko's hands, Nagito is fatally stabbed in the heart, Kazuichi chooses to gut himself rather than hurt Sonia, Hifumi and Twogami are both brutally killed by a Monokuma, Sakura is repeatedly blasted with a shotgun by Chihiro while Hajime is Forced to Watch, Ethos finds out his best friend and girlfriend are both despairs before losing an arm in an attack, the survivors end up scattered, the school is demolished with almost three thousand people still inside, many friends and family members of the students are taken captive, and we learn that 3 billion people worldwide have been brainwashed into becoming despairs.
What keeps it from being a Downer Ending that the fight between hope and despair is far from over. Junpei reveals himself to have been Good All Along, Class 79 survives the attack, Mukuro is sticking with her Heel–Face Turn, the Remnants of Hope find shelter with Sayaka taking up the role of The Leader, and the Future Foundation members manage to rescue a good number of the students, taking them to their island base where they can rest and plan for their rescue missions.
The Katawa Shoujo fanfic Reconciliation. Hisao dies of a heart attack, devastating both his wife Lilly and Hanako, and preventing Hanako from apologizing to him. However, Hanako and Lilly renew their friendship, and Hanako later gets into a relationship with her publicist Sho.
Sacred Reliquary leaves us with "evil" defeated as usual... but to prevent the cycle from repeating, Link chooses to destroy the Triforce completely, wiping all magic, magical beings, and the memory of such from the face of the earth entirely. And given the morally grey undertones of the fic, the results of the final battle are something of a Pyrrhic Victory.
Two of the alternate endings for the Sonic X: Dark Chaos rewrite are this. Ending A has Tails dying to stop Dark Tails, the galaxy left in ruins and the Forerunners invading the universe... but Sonic and his friends got their Planet Egg back and everyone joins forces to stop them. Ending D is the "happiest" of the endings - the above still happens, except Tails doesn't die which (while leaving Dark Tails alive) stops the Forerunner invasion entirely.
To-Love-Death, Mr Law's To Love-RuZombie Fic ends like this, Rito and several of his classmates and teachers survive, but not without most of the main Toloveru cast being killed off in horrible ways. Not to mention Nana making it all the way to the end before being decimated by helicopter blades by a surprise zombie. Turns out they didn't love death after all!.
In With Strings Attached, after successfully restoring the Vasyn to Ketafa, the four are informed that they can't take their magic home with them. Whereas John and Paul are pleased because they were fretting about returning to Earth as Blessed with Suck, Ringo is devastated, because he was profoundly transformed by his magic and had all kinds of plans for using it. He ends up clinging to the hope that the four will be given a chance to use it again in the future, making this a rare book where the characters actually ask for a sequel.
The Legend of Zelda fanfic, Zelda's Honor, has a rather depressing one. The majority of the Gerudo are killed in Link's purge of holy hellfire; all the Kokiri except for Saria are basically dead and she's left pregnant and decides to live alone in the woods raising a new brood of Kokiri; Malon had her son aborted in front of her and is now left a single mother of a future daughter; Impa and Talon are dead; Giana, Darunia and various other characters have lost limbs and are disabled for the remainder of their lives; Link dies alongside Navi by Zelda's hand to save the world from his righteous judgement against all who opposed Hylia and the Triforce. But hey, the good guys still won in the end, right?