In Futurama's "The Luck of the Fryrish", Fry, while trying to find a seven-leafed clover that gave him extraordinary luck back in the 20th century, comes across a glorified statue of his older brother Yancy, with Fry's clover pinned to his coat and Fry's name on his pedestal, which praises him as the first man to reach Mars. Yancy apparently was well-known as a heroic 21st century pioneer and adventurer, but everyone knew him by Fry's name: Phillip J. Fry. However, in Fry's memory, Yancy was extremely jealous of Fry and his luck in the twentieth century, and was notorous for stealing from him frequently. Fry is devastated, certain that Yancy stole his clover, his name, and his glory; as it had always been Fry's greatest dream to be an astronaut; using Fry's lucky charm to win his success. However, when Fry finds Yancy's grave and plans to rob it to get his clover back, he catches sight of the epitaph: "Phillip Fry, the Original Martian. Named in loving memory of his uncle to carry on his spirit." Fry then realizes that the Original Martian was not Yancy at all, but Yancy's son, Phillip Fry II, whom Yancy named after his younger brother, and presented with Fry's clover, declaring "I love you Phillip, and always will," to both of them. The episode ends with Fry kneeling tearfully before his nephew's ancient tombstone, while "Don't you Forget About Me" plays in the background.
This is even more meaningful when you remember that that Fry's father had told Yancy that all the first-born Frys are named Yancy.
There's also "Time Keeps On Slippin'," where Fry tries to figure out what he did to get Leela to marry him during the time skips. The crew deploys an explosive into the chroniton-filled nebula responsible for tweaking time, Fry notices that the stars spell out "I Love You, Leela," something he must have wrote during one of the time skips that won Leela over. Unfortunately, the explosion causes the stars to be sucked into a black hole, without Leela ever seeing the message.
A similar feeling is invoked in "Jurassic Bark", where Fry attempts to clone his pet dog, who had died 1,000 years previously, so as to 'have his best friend back'. By the end of the episode, however, Fry comes to the revelation that his dog was only a couple of years old, and had it died of old age then it would have been someone els's pet for longer than it was his, and therefore should be allowed to rest in peace. This is Bittersweet enough, however as the credits roll we learn that the dog loyally waited for it's Master to return, never moving from the spot until it died. It WAS Fry's pet and best friend all along, and he decided not to bring it back on a mistaken assumption. In fact this ending was such an immense Tear Jerker that the show's producers ended up receiving hate mail from viewers who had cried. However – possibly due to the aforementioned fan backlash – the ending was later retconned by the movie Bender's Big Score, which, due to time travel, allowed a time-displaced double of Fry to return to the past and pick up his life just how he left it, with Seymour at his side.
In "Yo Leela Leela", Leela admits that she was plagiarizing everything about her children's show franchise from the real Rumbledy-Hump. The producer decides to turn the show into a reality show. The Humplings go on to live better lives thanks to modern conveniences, and the orphans Leela tried to make happy with her show are adopted by the producer as his production crew. Leela herself, however, finds herself as a Karma Houdini demanding punishment for her actions as the episode closes.
South Park: "Lice Capades", "Over Logging" (hilariously).
In "Starcrossed", the final episode of Justice League, Earth is saved from destruction... at the cost of their home base, one of their members leaving (breaking up the series' main relationship), and an untold amount of the Thanagarians threatening the planet. Sweetened a bit by its continuation, Justice League Unlimited, which shows that things can be rebuilt, but even then there's a note of bitterness lingering throughout the series. Thanagar loses its war and planet, Shayera has to spend years slowly earning back the trust of Earth, can't earn back the trust of Thanagar, and the relationship between Diana and Shayera is one of the most strained in the League. At least Diana starts to warm up, and time travel shows that John does get back with Shayera.
Code Lyoko: The currently final season ends with the characters completely annihilating XANA. However, Aelita's father Franz, in order to allow the team to destroy the Big Bad, sacrifices himself shielding his daughter. Along with that, William is stuck with no memories of the few months of his time possessed by XANA, but the others have a hard time no longer seeing him as The Dragon. Finally, they decide to erase Sissi's memories after she finally discovers why they were so cruel to her for the last two plus years, request her friendship after the last Return Trip to apologize for said cruelty, and shut down the supercomputer, permanently destroying any iota of hope in saving Aelita's father.
Danny Phantom has two. "Public Enemies" ends with Danny Phantom completely hated by his hometown, staged by a vindictive ghost. Danny, however, regales in hope and continues to play hero (and eventually succeeds). "Flirting with Disaster" has Danny and Valerie dating happily, the latter willing to give up ghost hunting for Danny. Irony because while he saved the world, Danny [Phantom] himself caused Valerie to break up with him to further her career for his safety. Made even worse when Danny was just about to give her a class ring and ask her to be his official girlfriend. Ouch.
In Ōban Star-Racers, Eva and her ex-Jerk Ass father rekindle their relationship, the galaxy is saved from the Big Bad, and all the good guys get to go home. Well, except for one. Jordan Wilde, Eva's star-racing partner, becomes the Avatar and must stay behind on Oban to take care of the galaxy for the next 10,000 years, all after he confessing that he loves her. He is last seen crying as Eva's ship takes off.
Additionally, Eva's motivation for taking part in the first place, finding a way of bringing her mother back from the dead, was a pipe dream all along. However, she does learn to accept the loss by the end of the series.
The episode where Eva races Spirit, the creature she holds responsible for her mother's death, also ends on a bitter sweet note when she learns the truth of that day.
In the Beast Wars series finale, the Maximals finally managed to defeat and capture Megatron but at a heavy cost. The first Dinobot sacrificed himself earlier on to prevent Megatron from destroying the proto-humans. Depth Charge killed himself and Rampage in a final attempt to stop Megatron from raising the Nemesis(he didn't succeed, though he did get closure with his long-time nemesis Rampage). Tigatron and Airazor came back as one being, Tigerhawk, only to be gunned down by Megatron aboard the Nemesis in a last-ditch effort to stall Megatron. The Transmetal II Dinobot clone turned good but died a mere few seconds later after refusing to save himself from the exploding warship. Heroes aside, fans have even mourned the deaths of the Predacons as well, including Rampage, Inferno, and Tarantulas. And there were all the abandoned Stasis Pods that the comics had to deal with it. In the final scene with the Maximals, Optimus Primal even noted that victory had come at a cost, having lost so many comrades and allies.
By the final episode of Moral Orel, none of the Puppington family's problems seem to have been solved (in fact, they were probably made worse). The only thing that keeps this from sliding into Downer Ending territory was the Distant Finale that showed Orel eventually growing up and successfully starting his own loving, functional family.
Transformers Animated, "Endgame: Part II". On the sweet side, Megatron, Shockwave, and Lugnut have been defeated and detained, Starscream is dead, 2 of the 3 Constructicons are presumed dead, The Allspark is whole again, Arcee has her memories back, and Omega Supreme is back online. Not to metion it's heavily implied Optimus will become Magnus. BUT on the bitter side Starscream's Clones, Swindle, Lockdown, Blitzwing, Team Charr, and maybe Soundwave are still at large, Blackarachnia and Waspinator are still stuck in what may be the Earth's past, Prowl sacrificed himself to rebuild the Allspark, Ultra Magnus is near death, and Sari's origins are still sketchy at best.
Don't worry, the Allspark Almanac Volume 2 will probably answer these questions when it comes out.
If anything, it is even made more bittersweet, remember that Decepticon from "TransWarped" called Cyclonus? Entries in the Almanac pretty much make it clear he is from the future, where Megatron at some point becomes Galvatron. All of the battles our heroes had in the show were for nothing, and since it ended we have no way of knowing if everything turns out okay. Even worse when another entry implies Cyclonus is the future version of Starscream's cowardly clone. What kind of future could make THAT guy Take a Level in Badass? Most likely the universe's version of Unicron, but still.
Metalocalypse usually has ones of these endings where at least one person has died a horrible gruesome death if not an entire town or many many other people like the typical end to one of their concerts. (You'd think that if most of their fans keep dying from episode to episode there'd be no more fans left.) But hey, Dethklok survives unharmed from all adventures if not ahead.
The thing is, though, these endings are usually Played for Laughs. A straighter example would be the season 2 finale: Dethklok lives, and some even get to be heroes, but Mordhaus is burning to the ground and Ofdensen is in critical condition.
Then the episode 'Dethhealth': Pickles isn't dying, but Toki's cat has died, and Nathan's dentist committed suicide right in front of him.
The Secret Saturdays Season Two finale ends with the Big Bad vanished. The Cryptid war he started has also ended and everyone is alive and well. Except Van Rook who performed a Heroic Sacrifice for Drew Saturday whom he loved. Zak also loses his Cryptid powers, turning him into a normal boy.
6teen features one of these, involving Nikki moving permanently (at least until college, anyway) with her family to Iqaluit, Nunavut.
In the Jonny Quest: The Real Adventures episode "Ndovu's Last Journey," the Quest team successfully keep the poachers away in order for Ndovu (the titular elephant) to reach the elephant graveyard... so he can die.
Adventures of the Galaxy Rangers loved this one. About 1 in 5 episodes ended with the Rangers' "victory" being merely getting away with their shirts and souls intact. "Psychocrypt" and "Galaxy Stranger" are arguably close to a Downer Ending.
Wolverine and the X-Men. Yes, the Sentinel-ruled no-humans imprisoned-mutants future crisis has been averted; the Phoenix Force has been dissipated; and Genosha now has a new, kinder ruler in the Scarlet Witch. But the final battle cost Emma Frost her life, and Charles Xavier faces a new challenge after awakening from his 20-year coma: the Age of Apocalypse. Sure, this sounds like a great set-up for season 2, but the series has been cancelled, so yes, it counts an ending.
The original X-Men cartoon has a Bittersweet Finale "Graduation Day." Professor Xavier was hit by a Psychic wave that weakens him to the point of near death. After Wolverine, Cyclops and Jean were able to convince Magneto to send a message to the Shi'ar Empire, Professor Xavier said his good-byes to his X-Men (Morph included) and to Magneto before he dies. Empress Lilandra made it to resurrect Xavier so that he can be cared for with Shi'ar technology on their planet. The final scene involves Empress Lilandra taking off with Xavier for him to heal while Wolverine, Cyclops, Jean Grey, Storm, Jubilee, Gambit, Rogue, Beast, Morph and Magneto looking onward as the Earth itself face an uncertain future.
The finale of the first season of Avatar:The Last Airbender. Zhao is defeated (and killed) and the Northern Water Tribe is defended, but Yue must go to become the moon spirit, Iroh and Zuko are fully branded as traitors and have no one but each other, and Fire Lord Ozai has decided to become more proactive, and sends out his top enforcer, his daughter.
in The Animals of Farthing Wood, at the end of season 2, Bold returns home for the sake of his mate and unborn cubs. Because he was way to weak to make the long journey back home, He has to pay for it with his life.
A couple of seconds before he dies, he hears from his father that he is proud of him, so he can die in peace. also see "Well Done, Son" Guy.
Not even the original Transformers series made it out with (completely) happy endings. This was most evident in the series finale "The Rebirth, Part 3". Sure, Cybertron and Nebulos are saved, but the Decepticons aren't defeated - Galvatron and Zarak (and most likely their forcesnote Though only Cyclonus, Scourge, The Combaticons and the Targetmasters & Headmasters are shown boarding) survive and roam the universe inside Scorponok. It's also implied that Zarak will likely betray Galvatron. But due to declining interest, this was never expanded upon.
The second season episode "The Golden Lagoon" has the Autobots stopping the Decepticons from using the title pool's invunerability on themselves to conqueror the world. However, in the process the woodland paradise surrounding the Lagoon is ravaged. The ending has Autobot nature lover Beachcomber surveying the damage while mournfully declaring "We won."
Calamity Coyote's segment in the Tiny Toon Adventures episode "Career Opportunities" has him pursue Little Beeper for some pizza, until the end where the pizzeria offers free pizza. Just when you thought that Calamity would go hungry, he is finally given a slice... of hot chili pizza, hot enough for him to be escorted to the hospital by Buster and Babs.
The "The Beeper Queen" episode of Hey Arnold! ended in this. Helga's mom is no longer paying little attention to her due to her work, making Helga feel better and rekindling their relationship back to its old self. But now now Miriam's back to being a depressed alcoholic, who will probably go back to neglecting her anyway.
"Pigeon Man" has Arnold taking his sick pigeon Chester to Vincent (the eponymous Pigeon Man), an outcast with a fascination for birds. In return for caring for Chester, Arnold takes Vincent out for some pizza, and while that occurs, Harold, Stinky, and Joey head to Vincent's roof and trash everything, but not without being chased out by the pigeons due to Joey holding a spilled bag of bird seed. When Arnold and Vincent find out that the roof has been vandalized, they are distraught and Vincent decides to literally fly the coop with his pigeons to help other birds in need. Even though Vincent distrusts humans again, he still trusts Arnold and hopes to find another human being like him.
Vincent: Remember Arnold, always wash your berries before you eat them, and fly toward the sun.
Monster Allergy episode, "The Devourer" really has this kind of ending. The invasion of Bibbur-Si done by Magnacat is foiled, but Zick has lost his powers, including his ability to see monsters. There's good news in that: Elena can finally see monsters.
Young Justice's episode "Failsafe" ends with the team waking up from their comas as a result from the Unwinnable Training Simulation and the Justice League being alive but M'Gann is emotionally traumatized and weeping over what she has put the team through by accident and Martian Manhunter reveals to Batman that she has more raw power than himself.
The first season of Rollbots ends with Vertex and Vett's plan foiled and Vertex killed. However, he manages to take Captain Pounder with him.
Captain Planet infamous HIV episode "A Formula for Hate" has one if you think about it. While Todd was accepted by the townspeople, who learned that HIV positive people who need help and support and are not monsters and felt guilty about harrasing him, Todd still has HIV and will not get the chance to marry his girlfriend and have children, since they will also get HIV and Todd will eventually gain AIDS and die.
The Batman had episodes often end like this as time went on, but the first Bittersweet Ending in the series definitely had impact on the show; the two-part first season finale, "The Rubberface of Comedy" and "The Clayface of Tragedy". The Joker begins a crime spree with his Joker Putty, capable of turning anything into a putty-like material. When the police try to stop him, Joker kidnaps Ethan Bennett, Bruce Wayne's oldest childhood friend and an officer constantly harrased by Chief Rojas for thinking The Batman is good for Gotham City. At the end of the first part, Joker ends up mind raping Ethan and accidentally turns him into Clayface by exposure to gas based on Joker Putty. During the second part, Ethan attempts to exact revenge on Chief Rojas for his torment. Batman manages to save Chief Rojas, but is defeated by Clayface. Yin saves Batman, but Ethan escapes and is nowhere to be found, and since he can now shape-shift...Bruce feels he may never see his friend again. Of course, later he does in the second season...only for Joker to convince Ethan to not reform and instead embrace being a supervillain. At least in that episode, Batman caught Clayface this time.
Played for Laughs in "Swarm of the Century". Pinkie Pie is able to lure the parasprites away from the town, but it's still taken a lot of damage from Twilight's last botched attempt at stopping the parasprites from eating all the food (which caused the parasprites to instead eat everything except the food)
"The Best Night Ever" ends with the Grand Galloping Gala in disarray and several of the main characters' hopes for the night (Rarity meeting her Prince Charming, Applejack making money for the family farm, Rainbow Dash getting to hang with the Wonderbolts, etc.) dashed, but at least they're able to spend the rest of the evening with Princess Celestia and laugh off their bad night over donuts and cocoa.
An even more mild example occurs at the end of "Hurricane Fluttershy". Rainbow Dash has been assigned the duty of transporting the water from Ponyville's reservoir to the Cloudsdale weather factory via a pegasus-powered tornado. She not only wants to succeed in this task, but also beat the current tornado-wind-speed record of such a procedure. When Fluttershy finally overcomes her fear of performing and helps, she and the other pegasi succesfully transport the water, but still fail to beat the record.
The Teenage Mutant Ninja Turtles (2012) episode "The Gauntlet" ends on a somewhat depressing note. Sure, the Turtles managed to stop the Mutagen bomb from detonating and sucessfully fought off Bradford and Xever... But then the Shredder showed up and gave them all an absolutely brutal beatdown, with the Turtles only managing to escape when the Shredder was distracted by the mutating Bradford and Xever. On top of all this, April's father allowed himself to be caught whilst escpaing, so that the Turtles could go and stop them bomb.
Scooby-Doo! Mystery Incorporated ends with Scooby destroying Nibiru and saving Crystal Cove but in the process erasing it from existance, meaning that all of the crimes caused by its influence never happened, everyone's lives are better, and there are no mysteries for the gang to solve anymore. Then they get the CD...
Ben 10: Omniverse: Frogs of War ends with the Inkurseans defeated, or rather Milleus defeated, with Attea revealing she orchestrated his downfall, and has maneuvered the protagonists into a corner where their defenses are down. The Inkurseans, despite being scattered are firmly entrenched in Earth's sector, and will continue their oppression. Attea promises to remove the forces and pay for all damages, provided they let her go, meaning she'll be in charge of the empire (the last time she attained power, she tried to blow up Earth for fun; this time she's got the entire legion directly at her beck and call). Despite Ben's protests, Max concedes her point and lets her go (the alternative being prolonged Occupation and a possible power struggle). The ending with the Dating Catwoman and Take That Kiss can push this into Esoteric Happy Ending as the narrative leans to make it more positive.
The Legend of Korra, Book Two: Vaatu is destroyed (at least until the next Harmonic Convergence), Raava is reborn and re-merged with Korra, and the Water Tribes are at peace again... but Korra has lost her connection to past Avatars, effectively restarting the Avatar Cycle from scratch.
In Star Wars: The Clone Wars's fifth season finale, Ahsoka gets subjected to Kangaroo Courts. She is eventually proven innocent, but the Jedi High Council has alienated her to the point where she finds herself unable to return to the order. (Of course, her status as Anakin's padawan was Doomed by Canon in the first place.)
The G.I. Joe episode "Sink the Montana!". A historic U.S battleship is scheduled to be decommissioned, but its admiral (a long-time friend of General Hawk) is strongly attached to the vessel and joins Cobra to prevent it from being scrapped. The Joes ultimately capture the admiral (who decides to go down with the ship until Hawk punches him out of it) and the ship is sunk by the U.S. Navy. In the final scene, Shipwreck (another Joe who had sympathized with the Admiral) wonders what punishment the Admiral will receives and Hawk responds that he doesn't know what'll happen but that his friend already paid "the ultimate price", as they watch the Montana sink and explode.
Several episodes of Samurai Jack end this way, with Jack managing to defeat Aku's forces and save innocents from death or enslavement, but having to forfeit a chance to go home to do so. (Downer Endings in the series are quite common too, for that matter, but then, Jack never expected his quest to be easy.)
The Grand Finale of Daria leans toward sweet, since most of our main characters got into colleges they wanted and Daria and Jane are going to move to Boston together, but Kevin is being held back, Trent is going to be alone without Jane, Daria and Tom break up and Mack and Jodie are going to schools that are apparently far apart. Quinn's subplot is particularly bittersweet: she makes a friend who has a drinking problem, tries to confront her about it and the two have a big fight. The friend apologizes later, but she still does not acknowledge her problem and it's implied that, since they don't work together anymore, the friendship is not likely to last.