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 conforts Pikachu, reminding her how much she, Ash, and Brock all love him. Ontop 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 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 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.
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 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.
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
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.
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 suvives, 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 thier 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.
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 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 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.
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.
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 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")...
The Hunger Games fanfiction Some Semblance of Meaning has an ending that is very bittersweet. After tragically losing multiple allies in the Games, Vale herself dies in the final confrontation, in the act of defying the Capitol. Even the victor— former Career tribute Obsidian—ends up getting killed in a mining accident... after faking his own death and traveling all the way to District Twelve to meet Vale's family. Basically, a lot of beloved characters end up dead—though they do find peace in what Vale once dubbed the "place without districts." Meanwhile, Damon and Lavinia end up Happily Married in District Twelve, naming their children after Vale and her district partner Kit, while Vale's sister Laurel finds happiness with Glint, Obsidian's cousin, and both families escape the bombing of Twelve and survive the war against the Capitol. In the end, years afterward, Lavinia relays Vale's story to Katniss Everdeen, thinking that was what Vale would have wanted.
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.
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.