The end of the Golden Age Arc from Berserk. After Griffith's capture the Band of the Hawk is driven out of Midland and hunted as fugitives. Guts returns a year later and it seems that with his help they may be able to rescue Griffith and restore the Hawk's glory. They succeed, but Griffith is warped from torture and uses his behelit to initiate The Eclipse, which promptly kills the remaining members of the Band of the Hawk. With the exception of Guts, Griffith and Casca, the characters they've spent the entire manga so far building up are offed without much ceremony.
The Chapter Black saga from YuYu Hakusho could be considered an example of this. The characters pull out all the stops, sacrificing a great deal in the process, in order to try and stop Sensui from opening a tunnel to Demon World, only to eventually learn that A) Sensui's true motive for opening the tunnel was just so he could go to the demon world and find an opponent who could kill him, B) he would have been dead within a month anyway, from a fatal disease, and C) the spirit world's elite soldiers could seal the demon tunnel with relatively little effort.
CLANNAD After Story, before the Reset Button is hit, shamelessly goes for a shaggy dog shoot, taking the story from sad to abjectly miserable and pointless. Despite this, there are some who think this ending is superior to the True End.
Even though the end result is world peace, it comes at the expense of the destruction caused during the Zero Requiem, which, again, could have been averted had it not been for the above case. Not to mention that the resulting peace will not last more likely than not, and at the same time, Lelouch will still be dead, when he would be more useful alive as a leader.
Asano, the Unlucky Everydude from The Twelve Kingdoms has several of these moments in his plot arc. Despite being an Ordinary High-School Student trapped in another world, he is ultimately ineffectual in doing any good for himself or for his friends, and he eventually becomes a patsy of the Big Bad. Just when it looks as though he's about to redeem himself by performing a vital, heroic mission for the good guys, he gets intercepted by the villains, who kill him in spite of his being armed with a gun, while they only have primitive weapons. To further rub salt into the wound, Asano, before he dies, learns that his mission was completely unnecessary, since reinforcements were already coming to help the good guys.
Considering Asano wasn't part of the original book (and neither was his female counterpart) and the only reason for him to be there is to externalize Yoko's inner Tomato in the Mirror conflicts in the medial transition, this is hardly surprising.
Neon Genesis Evangelion (particularly its supplemental film The End Of Evangelion) is a borderline case: after Instrumentality/Third Impact, the Earth is left in ruins and everyone besides Shinji and Asuka is reduced to "primordial soup" with the choice to recreate themselves if desired (meaning that the whole plot caused more harm than good for everyone who would rather not live as part of a puddle of Tang).
In Rebuild of Evangelion, the third movie is this compared to 1.0 and 2.0. To sum it up: everything that happened in the prior two movies has been rendered moot because Shinji triggered Third Impact. It becomes clear throughout the movie that everything Shinji does to try to make things better ends up backfiring and making things worse for everyone, usually through no fault of his own. Little wonder he's in an Angst Coma by the end. The final movie will determine whether things will stay as they are.
Narutaru's anime adaptation. Most of the cast goes insane and dies in a generally unsatisfying fashion, except for the main character and the vaguely established villains, who vanish off the face of the earth around episode 10. Most of the plot points are Left Hanging, and noone seems to care much. The description that 'nothing much has happened except that a few ineffectual people has died' fits the story like a glove, although this is because the anime only covers the first half of the manga, cutting off right before things start to get really bad. The manga, incidentally, may also count as this.
School Days. After spending ten episodes acting like a complete jerk and taking advantage of the complete idiocy that seems to affect the entirety of the school, Makoto is stabbed to death by his pregnant ex-girlfriend Sekai, and then his corpse is decapitated by his girlfriend Kotonoha, who proceeds to murder (and cut up) Sekai and runs away, taking Makoto's head with her. Life at the school goes on, unaffected by the lunacy that just transpired.
The whole Fallen One arc in D Grayman is one of these. Allen encounters another Exorcist, Suman Dark, who has betrayed his Innocence by betraying the Black Order to a villain, and has been turned into a giant angelic torso-looking thing. Allen struggles to save Suman while he attacks mindlessly, killing a lot of innocent people. Allen finally manages to hold Suman back by over-activating his own Innocence, and he manages to pull Suman out of the monster... only for him to find that Suman has lost his soul anyway. Turns out Allen hadn't succeeded; Suman's Innocence basically timed out. Then, just to make things worse, Suman explodes in a fountain of blood, thanks to the sudden appearance of the villain from whom he begged for mercy in the first place.
Who then destroys Allen's left arm, punches a hole in his heart and leaves him for dead, because the arc just wasn't cruel enough as it was. Really, the only good things to come out of the arc is that Tincampy manages to escape with Suman's Innocence, and the destruction of Allen's arm eventually leads to him receiving a Next Tier Power-Up.
Gilgamesh ends with the deaths of the entire main cast against the villains, followed rapidly by all life on Earth getting wiped clean by a being who intended to reform the Earth afterwards, but is killed before it can recreate it.
Chrono Crusade (anime only), also a definitive example of a Downer Ending, ends with the main cast either dead or broken. None of the heroes' goals were met, and the villain succeeded in all his plans, with his "death" only being a temporary setback. If anything, the world would have been better off if the heroes had NOT been around.
The first season arcs of Higurashi: When They Cry are all like this; the audience are treated to several versions of the local True Companions going Ax-Crazy and murdering each other in various gruesome fashions, only for the "Groundhog Day" Loop to kick in and the whole tragedy repeated in a slightly different manner. The last arc seemingly subverts this, as Keiichi remembers one of the other realities and talks Rena down from her attempted mass murder/suicide... Only for Rika to get murdered anyway later, and the whole town wiped out by the volcanic eruption. Again.
Also from Higurashi, "Plan 34". A plan to kill thousands of innocent people in order to prevent a disease from causing a Zombie Apocalypse scenario is initially presented in the anime as evil, but better than the alternative. Then, the manga arc Onisarashi-hen shows that after the plan was carried out, infections started breaking out all over Japan anyways, due to people who had once lived in Hinamizawa but had moved away or were out of town at the time of the massacre. And then, because Higurashireally loves kicking you when you're down, it shows that the infection isn't as contagious as first thought and dies out on its own, demonstrating that the Plan 34 massacre was entirely unnecessary, and that the perpetrators were horribly misguided at best, or willing to intentionally kill thousands of innocents for political gain at worst. Isn't Higurashi wonderful?
It's even worse. The trigger for Hinamizawa Syndrome isn't distance from Rika, which the villains originally suspected; it's actually just extreme stress. In that case, their whole plan to wipe out the village through Plan 34 actually CAUSED the outbreaks in Onisarashi-hen.
Umineko: When They Cry does it in a similar manner. One example is a pair of climatic fights in the 4th arc, where the protagonists were about to win.
Tokyo Babylon, particularly when the continuation provided by X1999 is added in. After spending the series waiting to see if Subaru can inspire any actual feelings of love in him, and just when Subaru has realized his feelings for Seishiro, Seishiro decides that... no, he doesn't care about Subaru. So he tortures him, tries to kill him, and does kill his sister, leaving Subaru permanently broken with the heart's desire that one day Seishiro will kill him too. Except that when he tries to let that happen, he ends up killing Seishiro instead. And then he becomes the Sakurazukamori in Seishiro's place.
The anime adaptation of Requiem (marketed as Anal Sanctuary in the United States) has Yukina being presented with Cecilia, an angelic violin capable of opposing Cannone, the demonic violin that has driven Akio to...ahem...enslaving the female student body of St. Cecilia academy. Immediately after we see Cecilia, cut to a scene of Yukina and the priestess who presented the violin in captivity, about to be raped by Akio's possessed students, and Akio in possession of Cecilia. Everyone gets ruined, mission failed, do not pass Go, do not collect 200 pints of shit.
Kurokami ends with most of the cast dead and when everybody expects a happy life for the main protagonists, it's revealed that the curse is not lifted, and requires a sacrifice to save humanity which will nullify all the reasons why they were fighting. And even after that sacrifice, one genius concludes that it does not matter much since many other curses still exist so getting rid of one was not a big deal.
Lost Universe pretty much ends this way depending on how you interpret the Cut Short ending was supposed to turn out. Protagonists die while fighting with the Big Bad. But too bad, there are a few baddies left and now there are no people who have the abilities to defeat them if they show up.
YMMV since the ending was pretty ambiguous, but Wolfs Rainfinishes with pretty much the entire cast dying within the last couple of episodes, and they never reach the Paradise they're looking for. In fact, the only thing they manage to do is stop somebody else from getting to it; it's pretty disheartening when the entire 30 episode show was about getting there. It's kept from being a Downer Ending by implying that they've been reincarnated, or have been put back in the human world, or... well, something, but seeing as they were there anyway, it definitely counts.
Oh! Great wrote a self-contained arc in his H-Series Silky Whip Extreme called Junk Story, that is a pretty damn grim version of this trope. To Wit: The plot is that, 100 years before the story began, A super-powerful military robot called Gatt fell in love with a woman named Mariko. By being denied Mariko, Gatt took revenge on all of humanity, destroying most of civilization and forcing humans to live in fear. The first 3 issues are Mariko, revived as an immortal cyborg, teaming up with a gun-runner to try and destroy Gatt. Only, it's revealed in the last two issues that all of this was pointless; The world government has deliberately allowed Gatt to keep rampaging for a century, as even though they have cyborgs vastly more powerful than him, leaving humanity in fear of an external monster foe makes them easier to control. The end of the series involves Mariko being captured by Caligula, a powerful Ax-Crazy cyborg employed by the government, the Gunrunner-Turned-Love-Interest getting killed off, and Mariko being forced to become Caligula's personal sex slave. Not only does the ending completely invalidate every plot development brought up until that point, but it brings up even MORE questions that will never be answered.
While the overall series is not so grim, the 18th episode of Scrapped Princess ends with Furet getting killed in order to prevent Pacifica and the others from getting captured, only to have them get captured five minutes later anyway.
Katanagatari combines a horrendous character mortality rate with an epilogue that states the Thanatos Gambit that caused everything seems to have had no effect whatsoever.
However, it's not particularly depressing, since no living people actually cared about the plan one way or the other. From the little we saw of him, it's questionable whether even Shikizaki Kiki cared about it.
In Bakuman。, "Classroom of Truth," a work submitted for the main characters to judge, ends this way. The characters are put into a survival tournament to escape their classroom, and all of them die. Even the main character gets chased down and eaten by a doppelganger. Mashiro and Takagi note that it is the opposite of the typical Jump manga that value hard work and friendship, but having the main character die in spite of his efforts doesn't work.
Death Note in every adaptation sees the deaths of all major characters and many supporting ones, and leaves no implication that the world is a better place for any losses or sacrifices. If Ryuk's statement about Cessation of Existence is an Author Tract, this can't be anything but a Shoot the Shaggy Dog story; negative gain for everyone would be the only possible outcome.
To be fair there was one character who achieved all his goals and changed the world in the way he wanted - Near. And, debatably, L ultimately achieves his goals in every version, even if he dies in the process.
The Impel Down/Marineford arc of One Piece. Luffy breaks into the most secure prison in the world, makes grudging allegiances with SEVERAL old enemies in the process, undergoes incredible punishment and nearly dies from poisoning...all to save his brother Ace from being executed. It's said that he's sacrificing his lifespan again and again with near-constant uses of Gear Second, plus the treatment Ivankov gives him for the poisons. He then breaks OUT, makes it to the execution, reaches the platform against ALL odds with help from newfound friends, and ACTUALLY SUCCEEDS IN FREEING HIS BROTHER. After all that...it's some choice petty insults from Admiral Akainu that goad Ace into a fight when he and Luffy are about to escape, leading to Ace getting killed by taking a magma fist intended for Luffy. It's the first real time in One Piece where the protagonist DOESN'T accomplish his goal.
A villainous example happens in the Fishman Island Arc: Hody Jones is an extremely racist Fishman who uses energy steroids to gain the power to take over the island and eventually of mankind. He had also murdered the reigning queen of the time and frame it on a human in order to make sure he'd have a loyal following of like-minded thinkers. After going through massive beatings from Luffy, he is defeated and the truth of the steroids is revealed. It turns out they're a special candy of the royal kingdom that accelerates the aging process, to which he and his men had overdosed on; leading them to become extremely elderly men. Even if he did manage to defeat Luffy, which is very slim, seeing how he was effortlessly beaten, he'd be too fragile and weak to achieve his ambitions. Also having admitted to his direct hand in the murder, as well as his abuse of literally every single major life in the kingdom, has made sure he's not going to paroled or jail-breaked from his imprisonment anytime soon.
Fate/Zero ends like this, which shouldn't surprise anyone who is familiar with Fate/stay night, given that Zero is the prequel and sets up the scenario for Stay Night, but the details are heart wrenching. At the end, Kiritsugu is forced to destroy the Grail which he had banked all his hopes on because it had become corrupted. His wife is dead, he will never see his daughter again, and he has only a few years to live. Sakura is still with the Matou. Saber still blames herself for the destruction of her kingdom. Worst of all, the two major villains survive. The one ray of hope that keeps this from being the worst Downer Ending of all time is that Shirou has taken up Kiritsugu's ideal and will eventually make things better.
Shiki ends with about 90% of the cast getting killed off in horrific, pointless ways, and then the village of Sotoba, which most of the remaining living humans sacrificed their sanity to protect from the vampires, ends up burning to the ground. Oh, and the only vampire who survives is the one who engineered the entire thing.
Puella Magi Madoka Magica does this with Mami's unceremonious beheading (shortly after Madoka decides to team up with her) and narrowly averts it in the ending. After several episodes of ruining Sayaka's life and one episode of sending both her and Kyouko to the grave along with Mami, Homura is about five seconds away from becoming a witch and allowing Walpurgis to destroy the city; but then Madoka appears and uses her amped-up wish to undo most of the damage. Without this last-minute intervention, Kyubey—the Big Bad—would have been the only survivor. Yet, like Clannad, some people dislike this ending because it wasn't the comprehensively tragic one they were expecting.
Faust's backstory from Shaman King. He fell in love with a girl with an incurable disease, and spent 20 years developing a cure. When he did, they finally got married and moved into their new home...where she was promptly killed by a burglar.
Now and Then, Here and There starts with a happy-go-lucky boy named Shu who meets a Rei Ayanami Expy named Lala-ru. Suddenly she's captured by a viciously insane dictator time-traveling from the barren, war-torn distant future, along with Shu, who vows to save her from this hell. She can control water with a pendant around her neck...at the cost of her life. After she uses her water to defeat the dictator and bring water to the parched future, the two share one last sunset together before she fades out of existence.