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.
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 too 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.
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.
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.
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 2006 revival of Biker Mice from Mars ends this way. After the three-part episode "Once Upon a Time on Earth" concludes with Throttle, Vinnie, and Modo defeating the Catatonians, Ronaldo Rump, and their old enemy Lawrence Limburger for good, the final episode "Turf Wars" has the trio go back to Mars to end the drought that has been plaguing the planet. Upon returning to Mars, the Biker Mice find Vinnie's old girlfriend Harley, who unfortunately has become evil because she thought the Biker Mice abandoned her, and in the end, after coming to her senses and deactivating Stoker's invention the regenerator to prevent Olympus Mons from erupting, is supposedly killed.
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.
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.
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.
"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.
In "Game of Tones" a destructive noise is threatening the Earth, and it turns out Fry remembers the sound from the last day he was in the past. Throughout the episode, Fry wants to say goodbye to his mom one last time, but is continuously interrupted before he's allowed to. He doesn't get the chance before they figure out what the noise is, but Nibbler lets Fry enter his mother's dream from a few days after he was frozen. So while Fry does get his opportunity to say goodbye to his mother, in the present he's still gone and she'll never see him again after this.
In "Meanwhile" Fry steals a time button from Professor Farnsworth to make the perfect proposal to Leela. Since all of his time traveling made his watch off from the actual time, he found out Leela was coming to the spot he planned, but it was too late, as he had flung himself from the Vampire State Building. After a lot of deaths and rewinds to save him, his friends eventually save him, but he smashes the device, making everything in the universe except for himself and Leela frozen in time, and Farnsworth seemingly dead. The two of them slowly age, exploring the frozen world, until both are elderly. Then, it turns out Farnsworth was alive, but stuck in time, trying to return to the present. He fixes the button, and makes it so it will send them back in time. Fry and Leela agree to this, and the button press sends the show back to the beginning of the show, erasing everything that happens, but will repeat everything that had previously happened. So while Fry and Leela won't be able to hold onto the time they had together, they'll get to do it all over again.
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.
The "The Beeper Queen" episode 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 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.
The Intruder III ends on this note. As it turns out, the base TOM and SARA have been operating out of since the last one is actually a ship and the Sand Worms that were the title characters this time around were really trying to help the two. However, the planet is dying and while the ship is able to leave with the youngest of the sand worms, the rest of the creatures die with the planet.
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.
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.
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.
Book Three's ending sees Korra emotionally broken and confined to a wheelchair from ambiguous mercury poisoning while the season's main antagonists may have only been the tip of the iceberg, as many other members of the Red Lotus organization are thought to still be at large. However, Jinora is anointed an airbending master in a manner that heartwarmingly recalls her grandfather and Tenzin pledges that the re-established Air Nation will take on the Avatar's duties while Korra recovers.
The series finale. Kuvira was defeated, Varrick and Zhu Li have gotten married, and Korra and Asami have come out of the closet and started a relationship, but Republic City is in ruins, Asami's father dies just as he manages to make amends with her, and Bataar Jr. is heartbroken and devastated by Kuvira's betrayal as well as his own crimes.
The series 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.
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.
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.
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.
"Flight To The Finish" ends with the episode implying Scootaloo may never be able to fly, but she gains back her confidence, allowing her she and the rest of the crusaders to win the flag-carrying competition.
"The Lost Treasure Of Griffonstone" ends with the characters being unable to recover the lost golden Griffon artifact that when lost, turned the once-proud Griffon Kingdom into a decrepit, downtrodden ghetto, and when RD and Pinkie leave, the town is still in complete ruin and shambles, but with Gilda the Griffon undergoing a Heel–Face Turn, they're hopeful that Gilda can instead use friendship to help the other Griffons overcome their greed and help rebuild their society.
Eva and her father (who left her behind) 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.
Charlie Brown's All-Stars: Charlie Brown declines an offer for his team to be sponsored into a real league, the team loses their next game, and everyone gets mad at Charlie Brown to giving up their sponsorship and uniforms, but then Linus angrily tells them it's because the league wouldn't allow girls or dogs on the team, and, out of remorse for their unjustified anger, they make Charlie Brown his own uniform (out of Linus' blanket).
You're in Love, Charlie Brown: Right before the bus leaves, Charlie Brown gets a note from the Little Red-Haired Girl, saying that she likes him. But Charlie Brown now has to wait for the summer to end.
You're Not Elected, Charlie Brown: Linus wins the election for class president, but finds that the class president has absolutely no say in school bureaucracy, leaving Sally fuming that Linus sold out like all politicians.
You're a Good Sport, Charlie Brown: Charlie Brown wins the race, but doens't get the promoted prize, instead getting gift certificates for a free haircut, meaningless to him because his dad is a barber and doesn't have much hair to cut. To make matters worse, the original prize was tickets for the NFL Pro Bowl, but Marcy states they couldn't get them, either because they were too expensive, sold out, or they were turned away at the box office for being unaccompanied minors.
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.
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.)
Scooby-Doo! Mystery Incorporated ends with Scooby destroying Nibiru and saving Crystal Cove but in the process erasing it from existence, 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...
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.
Curse Of The Flying Hellfish: Grandpa has the paintings he waited fifty years to get taken from him by the US Government and returned to the descendant of the original owner, but he was able to triumph over Burns, and regain Bart's faith and trust.
I'm Spelling As Fast As I Can: Lisa loses the spelling bee, but she did it honorably, Homer proved himself willing to trade the love for the Ribwich for his daughter, and the residents still honored Lisa for making it as far as she did.
"Raisins" involves Stan crossing the Despair Event Horizon and joins a group of goths after Wendy breaks up with him. After Butters gives him a pep talk about how his sadness is "beautiful", Stan quits the goth group and gets over Wendy... for the most part.
"Lice Capades", "Over Logging" (hilariously).
The Spectacular Spider-Man prematurely ends with Spider-Man defeating the Big Bad and New York is safe. However, said villain apparently died in front of his son's eyes, who again is Spidey's best friend and now hates Spider-Man. Peter's social life also isn't any better, as he breaks up with his girlfriend to get together with his true love, only she is being manipulated to not break up with Peter's best friend. Oh, and the Big Bad actually survived and is boarding a plane to a tropical island.
The Zillo Beast Strikes Back is a mix between this and Downer Ending. The Republic manages to neutralize Zillo Beast, saving Coruscant from more destruction. Unfortunately, though, it was the last of its kind.
Altar of Mortis: The balance of the force is broken, and the Daughter of Mortis (the personification of the Light Side) is now dead, with the Dark Side dominating. Fortunately though, the Daughter manages to have her remaining life force transferred into Ahsoka, bringing her back to life after being killed by the Son of Mortis.
Citadel Rescue: The Republic strike team manages to escape from Lola Sayu, along with the hyperspace route coordinates. However, Even Piell died, and although his half of the info was memorized by Ahsoka, Tarkin doesn't want to share his half of the info with the Jedi, claiming he was under orders from Chancellor Palpatine to bring the info directly to him, while Ahsoka, was instructed to only share her half with the Jedi only.
Carnage of Krell: Krell is killed by Dogma for betraying the Republic, and the Republic succeeds in its campaign to retake Umbarra. Rex however, isn't in the mood for celebrating, as he is left wondering what the point of the Clone War is.
The fifth season finale, The Wrong Jedi, is mixed between this and Downer Ending. 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.)
In the Steven Universe, episode "Bismuth", Steven manages to prevent Bismuth from putting the Breaking Point to use acting on her genocidal ambitions and survives while promising her to finally tell the others what happened to her, but he has to bubble Bismuth to defend himself, and it's clear no one is happy to have to put their friend back in her prison.
The Super Mario Bros. Super Show: Normally, Bowser will escape when his plans fail, but in the episode "Flatbush Koopa" after Mario destroys the warp pipe leading back to Brooklyn preventing Bowser from going back there, Bowser reminds him that he and his friends are stuck with him. The episode ends with Bowser chasing the heroes while firing his magic wand.
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.
In "Down the Mine", both Thomas and Gordon are in disgrace for their misbehavior - the former had ignored the danger sign and fell down a mine and the latter fell into a ditch an episode earlier, and as a result, Thomas is banished back to his old station pilot job, and Gordon is scheduled for goods work and nothing else, but the two engines agree to form an alliance as they set happily home.
In "Percy's Predicament", Percy is sent miserably to the works after an accident with the trucks, while Thomas returns from the works after crashing the stationmaster's house two episodes earlier, and works happily with Toby and Daisy on his branch line. This may be a subversion since the narrator says "all are great friends", meaning that Percy may have returned from the works, unlike in the novel where it states "all three engines are great friends". The show likely altered this to avert Snub by Omission for poor Percy.
In "A Scarf for Percy", after an accident with the jam and The Fat Controller's trousers, Percy soon cheers up after being cleaned and is informed by Henry that the weather will be warmer the next day.
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 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."
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.
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.
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.
A deleted scene from the series finale also depicts Slipstream using an Allspark fragment to bring back Starscream for unexplained reasons. Had the scene been left in, and a fourth season greenlit, it could have seen Starscream making matters worse by leading a Decepticon splinter faction and * 6teen features one of these, the finale "Bye Bye Nikki", involving Nikki moving permanently (at least until college, anyway) with her family to Iqaluit, Nunavut (her father got his dream job).
starting a Decepticon Civil War.
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.
X-Men 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.
"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 season finale "Endgame" ends with the whole world being saved and everyone safe and happy... except for Kid Flash who sacrificed himself to save everyone else. Artemis fully changes from "Artemis" to her other heroic persona "Tigress", stating that "Artemis was Wally's partner". Cue waterworks from the fandom.