Planescape: Torment's best ending is as follows: you have regained your mortality, learned your true name, and brought your friends Back from the Dead... And now all your hard work pays off, as you get to die and go to hell to be punished for the crimes of the First Incarnation. (Of course, the entire point of the game was to figure out a) who you are and b) how to die... Which you just did. Just too bad the person you are is overall an irredeemable bastard.)
Conkers Bad Fur Day ends on a shockingly sad note. Conker defeats the Big Bad (or rather, what came out of him), and becomes a millionaire, like he always wanted to. The bittersweet part? Berri, the only person Conker truly cares for, is dead, and now Conker is left to be forced to rule a land of people that he hates. All Conker wanted to do was come home from a bad hangover and forget about it, but instead he completely ruined his life. The final speech he gives at the ending of the game is rather depressing.
Conker: So, here I am. The king. King of all the land. Who would've though that. I guess you know who these guys are now, and I certainly do. But I don't wanna know them. And yep, I may be king, and have all the money in the world, and all the land, and all that stuff. But you know, I don't... really think I want it. I just wanna go home, with Berri, and, I dunno, have a bottle of beer. *sighs* It's not gonna happen. It's true what they say: the grass is always greener, and you don't really know what it is you have until it's gone... gone... gone... *goes to credits*
The good ending to the original game sees Cole having stopped Kessler, but having to prepare for The Beast alone, what with his girlfriend dead, his best friend turned a traitor, and the whole disaster pinned on him by Moya.
The good ending of the second game is even more bittersweet. On activating the RFI, Cole stops The Beast once and for all, at the cost of his own life, and the lives of every other conduit on Earth. However, the plague that would wipe out humanity is gone, and the town of New Marais hails Cole as a patron saint. Also, the very last moment of the good ending implies Cole might not be dead. This is unconfirmed at the moment, however, but considering that there will be a sequel, it will most likely be revealed then.
Trinity Souls Of Zill Oll: In order to defeat Lord Balor, the only sword that can defeat him will wipe Areus from existence and no one will remember him.
Final Fantasy I ends with the undoing of the Stable Time Loop that necessitated the quest of the Light Warriors — and as a consequence, nobody, not even the heroes themselves, ever remember their deeds. Also, the main villain gets everything he ever wanted. He's alive, and apparently near to the Princess.
Even worse than FFI, Final Fantasy II ends with Leon leaving the heroes, saying too much had happened, and that things couldn't go back to the way they were. Dawn of Souls furthers this by showing off all of the dead characters from the game watching over the still living characters. Not to mention most of the world population has been killed off due to two superweapons. Lest we forget: the world is not irreparably damaged, and the population isn't all that bad off (only one city is well and truly destroyed). Sure, the psychological scars won't heal easily, but they never do.
The original Final Fantasy Tactics ends with Delita becoming king, but he kills Ovelia in self-defense after she attacks him and stabs him. He is left wondering if his friend, Ramza, came off better because he was free, while Delita is Lonely at the Top. Meanwhile, Ramza is still considered a heretic, and he and his sister are apparently dead. Olan attends Alma's funeral and thanks Ramza for all he did, and muses why he did all that despite knowing that he would always be considered a heretic by history. The extended cinema answers that by showing him riding in peace with his sister. Hundreds of years later, Olan's writings are discovered, and Ramza's name is finally cleared, and his deeds are finally known to the world.
Final Fantasy Tactics Advance ends with an ambiguous ending where the characters aren't sure if they've succeeded or not. Rather, they've succeeded, but the question is whether they did the right thing. The ending makes it seem like Ivalice and the real world are two separate universes, rather than having them replace each other. Also, post-game content makes it seem like either only Mewt went back to the real world, or duplicates of everyone except Mewt were left in Ivalice.
Final Fantasy Tactics A2 ends with the hero, Luso, leaving Ivalice for good, with all his friends behind. However, it's not explicitly stated that he can never return.
At the end of Final Fantasy VI, Kefka is defeated, but his death means the end of magic forever AND the deaths of every single surviving Esper (if there even are any surviving Espers by that point), and this is all after Kefka ruled the world for a year while destroying cities left and right with a magic laser beam. Not to mention that Shadow is left inside Kefka's tower as it collapses and is never seen again.
Final Fantasy VII doesn't clarify anything in the ending, save that Red XIII survived to father children. The Compilation has clarified this, but only by making it even more bittersweet. The world is saved, but it's still a screwed-up place, Cloud is still mopey, Aerith is still dead, and Sephiroth is still lurking in the wings and probably always will be. Advent Children ends with Cloud and his True Companionsgoing into Lifestream-purified water for redemption. They seem to end up okay, as well (Cloud being not mopey anymore, for example).
Final Fantasy VIII's Stable Time Loop goes on perpetuating itself: tales of Ultimecia's actions and her brief reign of terror passed down from generation to generation lead to the persecution of sorceresses, which in turn provokes Ultimecia into attempting to change the past and, when that proves impossible, to compress time. Squall and company's defeat of Ultimecia during Time Compression throws both Squall and Ultimecia into the past, where Ultimecia passes on her power to Edea and Squall provides Edea with the inspiration for SeeD. The immediate danger has passed, but Ultimecia's rise in the future is all but guaranteed.
Subverted in Final Fantasy X. The ending is heartbreaking: Sin is permanently defeated, thus saving Spira, but both Auron and Tidus vanish. However, a scene after the credits reveals the possibility that Tidus is still alive.
The player also had to sacrifice the Aeon they had painstakingly collected and leveled up. Yuna herself mentions in the sequel how she still suffers from that.
Final Fantasy XIII: Lightning and co. manage to defeat Orphan once and for all, except that means that Cocoon is set to fall, killing everyone. In a moment of heroism, Fang and Vanille stay behind and use Ragnarok to save Cocoon, creating the Crystal Pillar, at the cost of themselves. Lightning awakens, and Dajh and Serah appear to reunite with their loved ones.
The ending of Final Fantasy XIII-2 goes all over the place with its ending. At first, it is a Happy Ending with the timeline fixed of all paradoxes, Hope managing to get the New Cocoon to float in the sky, Fang and Vanille's crystal rescued out of the Crystal Pillar before it collapses... and then Serah sees the changes of the timeline and dies in Noel's arms, making this bittersweet... and then things got worse. However, it is shown that Lightning will eventually wake up, and that the rest of the main cast lived to the sequel, and we'll see where it goes from there.
Secret of Mana ends with the world saved, but at the cost of the source of the world's magic, one of the three companions, the living Global Airship, the life of the female character's love interest, and most of the other connections to the world's deities. The world itself even splinters. Legend of Mana spends most of its time trying to simply repair the damage.
Seiken Densetsu 3 ends happily for everyone except your Exposition Fairy, who was killed by the Big Bad... but because she died at the base of the Mana Tree, this means the Mana Tree will grow back and someday she'll be given life again.
The three main story arcs in Legend of Mana all have bittersweet endings: The Jumi are restored to life by the Player Character's tears, and learn to cry themselves to un-petrify you, but it's highly suggested that the same tragic events that drove them to extinction will repeat themselves eventually down the road; Matilda dies and is restored to her youth, but her demon BFF Irwin rejects their relationship because he believes them to be fundamentally incompatible and she becomes a Wisdom for all eternity instead, and along the way one of your childhood friends went insane and you were forced to put them down; and the Dragon Crystals are restored to their rightful place, but Larc is condemned to wander the Earth until Draconis' curse wears off; he does reunite with his sister eventually, though.
Sword of Mana also ends with the Big Bad defeated, but it is revealed that the Mana Tree is the Heroine's mother, and she in turn becomes the next tree.
Bahamut Lagoon ends with one third of the story's principal Love Triangle dead and another mentally scarred and wandering the world alone.
Front Mission loves these: In the first, for example, sure, a couple rogue squads from the universe's two key supernations have uncovered and shut down a plot to make computers for Humongous Mecha from human brains — doesn't mean the third party occupying Huffman Island as a peacekeeping force will make the information public. Or that they'll let the island govern itself free from the corruption of all the military forces that have come through. Or that the player character gets to get his wife back, as he chooses to detonate his wanzer that contains her mind.
In the third game, Alisa, Kazuki's adopted sister, dies at the end of Emma's scenario. She stayed behind to ensure them enough time to escape the Ocean City before the MIDAS bomb vaporized the island. Kazuki and Emma are devastated, but a final email sent by Alisa before her death gives them the strength to move on. Emma and Kazuki are then seen in the field of flowers where Emma and Alisa used to play in, planning to start a family together. Alisa's scenario ends happier, as Emma and Alisa survive. However, at the end a pair of unseen scientists are discussing how they will breed the "new" set of Imaginary Numbers, and the door shuts behind them...
Fatal Frame lives and breathes this trope. All of the endings are designed to twist your heart, because no matter which ending you get – even the happier ones – someone has still lost or had to do something that has either contributed to their death or given them lasting scars. It's made even worse in that the canon endings to the first two games border on Downer Ending: neither Miku nor Mio have completely moved on from the events of the previous games, and Mafuyu and Mayu's deaths have left them with either Survivor Guilt in Miku's case, or with These Hands Have Killed and My God, What Have I Done? in Mio's case.
The ending of the first game has Mafuyu remaining behind with Kirie to keep her company as she keeps the gate closed to prevent the Calamity from happening while Miku escapes, leaving her beloved brother behind.
Crimson Butterfly ends with Mio strangling Mayu and her turning into a crimson butterfly. While this calms the Hellish Abyss and also frees the ghosts who have been trapped because of the Repentance, the fact remains that Mio killed her sister and has to deal with the fate of being a Remaining.
Mask of the Lunar Eclipse continues the tradition. Ruka remembers her father's face and sees him again one more time before he crosses over, but Misaki's fate is left up in the air, Choushiro comes back and places the complete Mask of the Lunar Eclipse on Sakuya which allows everyone to pass over. That does not change the fact that he's still dead along with pretty much everyone in the game.
Halo trilogy: The remainder of humanity has been saved, the Covenant has been disbanded, Gravemind and the Flood are toast, but at the cost of every named human we see in the games, except for Lord Hood. Including Sgt. Johnson (SAD SAD dirge music). The protagonist and his Ninja Butterfly are stranded at the edge of the galaxy, presumed dead.
In a presumably canon Halo novel (because they rehired the author, thrice), The Fall of Reach had a way to bring back people who weren't ''too'' dead via Applied Phlebotinum.
Given that Johnson and Keyes were completely incinerated in the center of a blast that was supposed to eliminate all traces of life in a radius of many lightyears far outside the galaxy, it's rather unlikely to work.
The first Halo had this as well. The ring is blown and the galaxy is saved. Too bad nearly everybody in the game was on the ring at the time, and Master Chief had to kill Captain Keyes himself after the latter was turned into a Flood monster. Sergeant Johnson made it off in a Pelican, but we didn't know this at the time.
Adding to the bitterness of the ending, billions upon billions of people are dead on both sides, a good majority of Human colonies have been glassed, and it may take decades to rebuild.
And "good majority" means "virtually everything but Earth itself". By this point, the total human population in the galaxy is estimated to be around two-hundred million, down from tens of billions at the begining of the war. Word of God suggests that 23 billion (out of 30-40 before the war) humans have died.
The Applechasers catch up with Giygas as he is taking form, and manage to bring Niiue and Giegue back together as one being with the same force that tore them apart. However, Giegue admits that his sanity is only temporary, and helps the party escape before he returns to his madness, leaving the heroes forgotten but safe in a different time while starting the events of EarthBound.
Lucas was forced to fight his reanimated, mind-controlled, twin brother, Claus, who he hasn't seen in nearly four years. He and his dead mother are able to wake him up, and he promptly kills himself in order to join their mother in the afterlife. And then, Lucas pulls the final Needle and wakes up the Dragon, which ends the world and either creates a new one or killed everyone in the game, leaving them in the afterlife. The game leaves this up to interpretation. Whatever happened, in the epilogue, the characters talk to the player and claim that they are all fine. If it turns out that another world was created, that means everyone survived, and all evil is washed away for good. But even then, it's a bittersweet ending, as it seems that everyone who died before the needle was pulled stayed dead, and the villain is still alive, but can't harm anyone now. But, Hinawa's spirit proves that there is an afterlife, and eventually, Lucas and his remaining family will join Claus and Hinawa in the afterlife.
In Betrayal at Krondor, the Great One Makala and real Big Bad is not evil as much as doing his best to fulfill his duty to protect the Empire of Tsuranuanni from what he misguidedly believes a threat, while being rather colourfully pragmatic in typical Tsurani Great One fashion. And the moredhel (dark elf) Gorath, the Noble Demon/Anti-Hero who's lost and sacrificed the most without even the barest complaint, even going as far as joining the sworn enemy of his people in an effort to protect them, and the actual hero of the story, has to be wastefully killed in a heartwrenching Kill Us Both moment by the very human he has befriended against all odds. Had he survived, he would have been free to live the rest of his days peacefully in Elvandar with the light elves, or return to what still remains of his clan and try to put the pieces back together, and perhaps even start to lead the moredhel people to adopt less murderous, saner ways. It's a loss alright.
Tales of Phantasia ends with the heroes defeating the Big Bad... but then finding out that rather than being evil, Dhaos was just trying to keep his world alive. In which case the heroes are feeling slightly less heroic than they'd thought.
Sticking to its Darker and Edgier nature, two of the endings in Tales of Xillia 2 are like this. The normal ending has Elle sacrifice her life to save the world, while the true ending has Ludger do the deed instead.
Terranigma ends with a real Tear Jerker - hero Ark manages to restore the world and defeat all the baddies... in the process destroying his hometown and himself as well. The final credits sequence shows Ark, in one last gift, flying the skies as a bird. On the other hand, the game's emphasis on reincarnation keeps this from being more of a Downer Ending.
In The Legend of Zelda: Link's Awakening for the Game Boy, the entire island turns out to be a dream that vanishes when the Wind Fish awakens. By completing the game without dying, there's a scene where the closest thing to a love interest is shown flying off with the wings of a seagull like she always dreamed.
The Legend of Zelda: Ocarina of Time ends with Link defeating Ganon in one timeline, and it is implied that he stops Ganondorf's plan before it can start in a second, but he is left with the memories of his battles and a hellish world ruled by evil that only he remembers, none of his friends in Kokiri Forest remember him anymore, and his best friend, who stood by him in every battle, leaves him for parts unknown as, having no memory of the alternate timeline, she feels that she is not needed anymore. Then there's the third timeline, which veers straight into Downer Ending teritory when Link fails to defeat Ganondorf and is killed in the process.
The Legend of Zelda: Majora's Mask seems to have a pretty cheery ending for what is otherwise a very dark and depressing entry in the franchise. The land of Termina is saved, the moon has been destroyed, the evil within Majora's Mask is gone, and the festival commences - with Link apparently being coerced into leaving before it even begins by the very people he had accompanied on his quest. But right after the scene where everyone you've helped is having a good time, you see the Deku Butler kneeling in agony before the dead, twisted tree you encountered at the very beginning of your journey; the one you saw right after being turned into a Deku Scrub. Tatl even remarked on how much it resembled your new, twisted form. When you wear the Deku Mask, the Butler is reminded of the days when he raced against his son, whose wherabouts are unknown throughout the course of the game. Remember, every other transformative mask you acquire in the game (sans the Fierce Deity's Mask) contains the spirit of someone who had died. Was the Deku Mask really an exception? And to top it all off, Link never actually manages to reconnect with Navi, who had left him without anything in the way of an explanation at the end of Ocarina of Time.
The Legend of Zelda: The Wind Waker: Ganondorf is finally and utterly defeated, but the Master Sword and the ancient Kindgom of Hyrule fall into permanent oblivion, despite it originally being one of your (unknown) goals to revive it. Also, King Daphnes rejects his grand-grand-[...]-grandaughter Tetra's pleas to go and search for a new land along with her and Link, resulting in him saying a touching line of speech, before finally drowning in the waters of the Great Sea, which crash down on the ruins of ancient Hyrule. Even Link tries to reach out for his hand once again, but he refuses to take it.
The Legend of Zelda: Twilight Princess ends with Link and Midna (who have become rather close friends after spending the bulk of the game practically inseparable) separated when the bridge between their worlds is permanently destroyed, and the populace at large is nearly totally unaware of the struggles the two went through. In this case it was done on purpose by Midna, apparently to make sure the two worlds remain separate and nothing like what happened with Zant ever happens again. This was a very unpopular move among Midna's many fans.
The Legend of Zelda: Skyward Sword ends with the sealing of Demon King Demise, bringing peace to Hyrule and the Sky. However, after his defeat, Demise curses Link and Zelda by encasing them and their descendants into an endless fight between good and evil, effectively setting up the existence of Ganon in the other games. Later on, there's the farewell between Link and Fi, then between Impa and Zelda in the past,and thenthe physical departure of Impa in the present.
Punch-Out!! for the Wii only truly ends after "Mac's Last Stand": after losing three times, Little Mac retires from boxing. The game ends with his coach, Doc Louis, walking through a museum which commemorates the highlights of Mac's career. Doc wistfully says "Good job, son...good job" while gazing at an iconic picture of himself and Mac biking/jogging.
Klonoa: Door to Phantomile ends with a Tomato in the Mirror reveal where Klonoa's best friend Huepow reveals that he faked all of their memories and pulled Klonoa in to save the world from another universe, and that he has to be kicked out to fully repair the world.
Klonoa 2 isn't much better. Sure, the main antagonist is killed and the world is saved, but the main antagonist turned out to be an Anti-Villain who only wanted to save his dying kingdom, and despite forming a close romantic relationship with the lead female character, Klonoa can't stay in this world either, and has to leave in an ending almost as heart-wrenching as the first game's.
Although the girl is brought back to life, Wander dies just before she wakes up, and his body is "borrowed" by Dormin as part of the terrible price Dormin warned him about in the beginning of the game. Lord Emon (the "bad guy, I guess") casts a spell that sucks Dormin into a giant pool of light, and because part of Wander is in Dormin, he gets sucked in as well. The girl wakes up to find a crying baby (which is implied to be Wander), and goes up to the Secret Garden to live happily ever after, maybe. Or she dies again, who knows. Also, the baby, according to the director, is a direct ancestor of Ico, hero of the previous game by the same company. That girl? She's implied to be the White Queen from Ico. The White Queen was the game's Big Bad. Judging by the caskets lining the walls in the castle in Ico, generations of children have now been doomed to suffer the curse brought upon by Wander.
Even more so, especially If one assumes that Mono found out everything about Wander's in-game actions (as implied through the credits vision according to Word of God), realizes that the horned infant she's been led to is him and once loved or cared for him to varying degree. If you assume that their relationship was that they were lovers, she's stuck alone in a land cut off from the world she once knew, forced to be a surrogate mother instead of a lover/friend. In addition, the infant 'Wander' may never grow to remember or realize what he once did, and the repercussions will haunt him and Mono for the rest of their lives.
Shadow Hearts 2 ends with the hero finally deciding to let himself die rather than allow the curse he's under to take his soul and memories. Not to mention the team is split up, they have just taken the life of the sympathetic Necessarily EvilBig Bad, and the world is a decade or so away from WW2. Though there is an upside — Yuri is sent back to the beginning of the first game by his dying thoughts, and it's implied that this time he'll be able to save Alice from the curse of the Four Masks.
The first game ended sadly as well, though not quite so finally. Simply put: "she" (you know who) dies to save his soul from being devoured. Yuri's soul sure comes under fire a lot...
Shadow Hearts 3 ends with the heroes discovering that the Big Bad "Lady" is actually the main character's sister, Grace, resurrected in body but not in soul. Contrary to RPG conventions, there is no way to actually save the sister, and in the bad ending (yes, there's one worse than being forced to murder the main character's sister) the Malice that powers Lady and her cohorts - and that she used to resurrect Killer, Edna Capone, Shania, and Johnny - corrupts the main female character. The Shadow Hearts series doesn't go for happy endings.
Koudelka. In the official ending of the game, one of the three main characters sacrifices his life to defeat the Big Bad, and the other two (who have spent most of the game flirting) wind up going their separate ways. And, of course, the central character from the game shows up again in Shadow Hearts, having been captured by witch hunters and locked away in an asylum, where she is tortured for years, which effectively orphans her only child. And then Yuri rescues her.
In the Left 4 Dead & Left 4 Dead 2 DLC mission "The Sacrifice" (and the comic tie-in), the original surviors escape to the Florida keys and potential safety from infected, but at the cost of one of their team members; while the players can choose between themselves in-game, the canon choice means that Bill Overbeck has been Killed Off for Real.
In Call of Duty 4: Modern Warfare, the British SAS/United States Marine Corps task force manages to stop the nuclear missiles headed towards the Eastern Seaboard and kill Ultranationalist leader Imran Zakhaev...but at a great cost. Most of the SAS/USMC team is executed seconds before Loyalist reinforcements arrive, and it isn't immediately clear whether your commanding officer or you, the player character will even survive (though the sequel reveals they pulled through). In addition, Al-Asad was captured and killed, but not before he detonated a nuclear device that killed 30,000 American soldiers and leveled an entire city.
In the sequel, Modern Warfare 2, things go From Bad to Worse. Soap and Price manage to disable and kill General Shepherd, but it's a hollow victory at best. The chain of events that started with an undercover agent posing as a Russian terrorist (and subsequently dying after being found out) led to a ground invasion of Russian forces in Virginia and Washington, hundreds of troops being killed, sweeping military powers being authorized and virtually an entire task force of elite troops being decimated before Shepherd was finally brought down. Soap and Price may still be alive, but the U.S. is on course for a major world war with Russia.
In Modern Warfare 3, by the end of the game the war between U.S. and Russia ends at a heavy cost with Soap dead by Makarov; Sandman, Grinch and Truck of Delta Force KIA and during the final mission to kill Makarov, Yuri is gunned down by Makarov, but Price manages to strangle Makarov to death with a steel wire and leave him hanging on the roof. The Good News is that all the evil men responsible for this are dead, Task Force 141 has been cleared of the bogus charges of treason and terrorism, and relations between the US and Russia finally evolve into peace.
In general, the Law and Chaos endings will lean more toward the "bitter," with whatever the conflict is being resolved permanently, but at the cost of thousands (at least) of lives and with yourself typically made a servant to morally dubious gods and/or demons. Neutral endings tend more toward "sweet," with both the Law and the Chaos factions beating a hasty retreat and humanity free to rebuilt, but this solution is usually noted to be temporary and the Forever War will begin anew, albeit with another hero likely to appear when that happens.
Shin Megami Tensei I. In the Law and Chaos paths, you achieve the goal of whichever faction you sided with...but nuclear war has left the planet in a state of disrepair, Tokyo has been flooded to death by God, and both of your best friends are dead—one either due to not being able to handle a powerful artifact or due to mortal conflict with the other, and the other thanks very much to you. In Neutral, you set out to pave the way for a new world that balances order and chaos...except you've made enemies of both the Messians and the Gaians and murdered both of your best friends.
Persona. When the main heroine has to disappear in order for the world to go back to normal, it says a bit about the ending (albeit the bad one—made worse that it isn't so much as a on-her-own-will sacrifice as it is forced).
Persona 2: Innocent Sin, which ends as a pure Downer Ending, and Eternal Punishment is cleaning up after Innocent Sin. Which leads to less dramatic results, but still ends with the same tragedy of the close knit friends of Innocent Sin losing their memories and friendship. The final scene is of Maya and Tatsuya, the characters who loved each other the most and whose tight-knit relationship was the entire crux of both games, acting as total strangers. All of this is necessary - if they ever remember each other, the world will end again.
The "good" ending results in the sealing away of a life-extinguishing monster that saves all life on Earth... But the main cast — with one exception — lose all of their memories of the Dark Hour and the year you spent exploring it, which takes with it all their significant Character Development, their memories of each other, and a whole lot of ugly — but necessary — truths. The cast are rendered casual acquaintances with little familiarity with each other; unaware of the struggles and personal victories they went through to save the Earth, save for flashes of Wistful Amnesia. In addition, the main character had to perform a Heroic Sacrifice to perform the sealing and dies just as the game ends — mere moments after the rest of the cast recover their memories and rush to his side.
In The Answer, the team is shown what really happened during the final battle — they witness the protagonist's soul being sealed in stone, becoming the seal that blocked the death monster Erebus from carrying out the fall of the world. After the battle with Erebus, the Abyss of Time dissipates, and the seal locking the party within the dorm disappears. The game ends with Aigis deciding to return to school with the others. However, they have realized that the protagonist has to remain as a seal for eternity, because they can never get rid of humanity's desire to die. He can never return to them, and they can only help him bear the burden by making the most out of their own lives.
The 'bad' ending is even worse. You decide to kill the avatar of Death's mortal body at his own request, but that won't stop him causing the end of the world, it will merely make you and everyone else forget long enough to enjoy the last few months of life. The game ends on the same day as the good ending, except everyone still doesn't know each other, have separated into their own cliques, and are enjoying a silly afternoon of fun, when the screen slowly fades to black...
Persona 4 has a certain scene where Magaret informs the party that she's there because Elizabeth went off to find a way to rescue the hero of Persona 3. Considering how ridiculously powerful Elizabeth is if you break the rules of engagement, there's a good chance she'll manage just fine in that regard.
Oni ends when you kill Konoko's brother, Muro, and interrupt his plan to poison the Earth's atmosphere, killing everyone who doesn't have a Daodan Chrysalis... by only poisoning most of Earth's atmosphere, giving humanity (now decimated) enough time to adopt the chrysalises. Whether this actually succeeds or not is left hanging.
In Fallout, the Vault Dweller may have saved eight settlements from a race of genetically-engineered super mutants, not to mention single-handedly fixing most of those settlements' social problems, but the Overseer of Vault 13 banishes him from his home because his time outside has changed him, and he's brought ideas and stories that endanger their peace and serenity. If the Vault Dweller got the Berserker or Childkiller karma traits, or you took the "Bloody Mess" trait at character creation, he shoots the Overseer in the head before leaving. You can also actively choose this by initiating combat and firing before he gets all the way into the Vault again.
The canonical first ending is bittersweet: the protagonist's sister and best friend are dead, and the dragon pact-partner he had grown close to is now the new seal. The third ending could also be considered bittersweet since the dragons have decided to exterminate humanity, but the protagonist has just killed the strongest dragon in the world (his pact-partner) and can probably take them. He certainly looks forward to it.
In the sequel's first ending, Legna reveals to Nowe that he is just a tool of the dragons, created from the bone casket as "the new breed", who will rise up and destroy the nameless (the Grotesqueries), thus allowing the dragons to take over the world and sentencing humanity to a gruesome fate. Nowe, deeply saddened by the betrayal of the one who raised him practically since birth, decides to Screw Destiny and kills Legna in the final battle, out of love for Manah and his desire to live as a human. But, to restore order to the human world, his former knight partner Eris gives up her normal life to become the new Goddess Seal, like Angelus and Furiae before her. The second ending has Manah offering herself to the bone casket and becomes possessed by the gods again, and Nowe kills her, as Manah will no longer be a puppet of the gods. However, Nowe and Eris decide to follow with Legna's plan to battle the gods. The third ending is the happiest, although Nowe kills Legna like in the first ending, but Manah fights off the power of the bone casket, freeing her from the gods' possession, and now the world has no need for the Goddess Seal, the dragons, and the gods.
Silent Hill games often end on a bittersweet note, depending on what you did during the journey.
Silent Hill 1: Even the Good+ Ending is bittersweet. Sure, Harry has defeated the Big Bad and saved the cop, but the little girl he worked so hard to save is gone, having been reborn AGAIN in the form of an infant. The third game reveals that Harry contemplated killing said infant to prevent Alessa reawakening on several occasions, but held back due to his love for Cheryl. And apparently his love for Alessa/Cheryl kept the cult's god within the girl's body in stasis for over ten years, as it feeds upon pain and hatred.
Silent Hill 3: The Good Ending has Heather finally defeating the cult's summoned god...only for her to break down crying afterward because her adoptive father Harry is dead, and while she's avenged him, he will not come back.
Silent Hill 4: The "Death" ending shows Henry stopping Walter's 21 Sacraments from being carried out, and the apartments return to normal. It appears that Henry is the only tenant still alive, and he is deeply saddened, as he could not save Eileen during the final battle.
Every ending except the Normal Blood ending in Book of Memories.
Pure Light: You decide to atone for your selfish uses of the Book by using it only to help others, but the final scene heavily implies you use a portion of your life force whenever you do so.
Normal Light: You resolve never to use the Book again and to make sure it never falls into the wrong hands. However, you slowly begin to become tempted by the Book's power once again...
Neutral: You're freed from the Book's influence, but the whole ordeal has shattered your mind, and you are sent to an asylum.
Pure Blood: With the Book's powers, you greatly improve your life, but quickly realize that it's Lonely at the Top.
Sonic Adventure 2 has an extremely Bittersweet Ending by having it where Shadow sacrifices himself to save the Earth and to accomplish his promise to Maria. Subverted in later games, when it turns out Shadow survived and Eggman's robots found him. The worst that happened to him afterward was a case of Laser-Guided Amnesia, from which he recovered.
In Sonic Unleashed, after Dark Gaia is stopped, Chip/Light Gaia seals himself along with the beast in the Earth's core.
And back in Sonic Adventure, Sonic got Perfect Chaos to calm down and stop being the destroyer of worlds... but by this point, Station Square was already flooded and in ruins. And it gets worse, with some Fridge Horror: the city was flooded/destroyed over the course of a few minutes, so it's likely that most, if not all, of the people living there couldn't get away in time.
In Disgaea: Hour of Darkness, you get different endings based on how you beat the game. In the default ending, which assumes you accidentally kill at least one teammate — pathetically easy to do due to the large area of effect attacks in the game, — Laharl, Flonne, and Etna show up to warn Seraph Lamington of Vulcanus's plan, and talk about Demons. He agrees that Demons are capable of love, but because Flonne has "betrayed" Celestia by fighting angels, she has to be punished, so he kills her (by transforming her into a flower). Laharl, enraged at this, attacks. Up to this point, the endings are the same. In the "normal ending", Laharl kills Seraph Lamington, only to have Mid-Boss appear and reveal that it was a test to see if Laharl would forgive Lamington; because he did not, Flonne is doomed. Laharl, distraught, either picks up Flonne's flower and exiles himself (asking Etna to rule in his place) for the rest of his life, or sacrifices his own life to restore her (On a slightly happier note, he comes back as a Prinny). In the good ending, which is considered canon, Laharl knocks Lamington out, but decides that Flonne would not have wanted him to take revenge. As such, Flonne is restored to life as a Fallen Angel — but is still her ditzy self. As a fallen angel, she can stay with Laharl and Etna, whereas as an Angel, she would have to return to Celestia.
In Phantom Brave, yes, you save the world, but Castile's brother Walnut sacrificed his life to beat the Big Bad, and Ash is still dead. A phantom, yes, but dead.
Some of the endings of Tactics Ogre The Knight of Lodis are quite the Downer Endings. In one of them, the hero's lover sacrifices herself to kill the Big Bad, the hero's best friend dies thanks in no small part to the hero, and said best friend's father, a duke, sends his army after the hero, forcing him to go into hiding. The game's secret ending (who is also the canonical one) is hardly any better, as all of the above happens and the hero is rewarded by the pope for killing the Big Bad with a new name, Lans Tartare, which reveals to fans of the series that this game was a prequel, and that the hero is an antagonist in Tactics Ogre: Let Us Cling Together.
Also in Tactics Ogre Let Us Cling Together, the endings wind up this way. If Denam becomes the ruler of Valeria, then it's because his sister (The rightful heir) is dead. He unites Valeria...but depending on your chaos frame, is either defeated by Lodis when they invade, or assassinated by a terrorist. It's better if Caitua/Kachua is still alive, then she becomes the ruler of Valeria. But in a thousand years, the Hittites invade Valeria. The PSP version tones this down a little by instead saying they "united" with Heth (Likely where the Hittites came from) and it sounds like the union was more consensual.
Super Robot Wars Original Generation ends with the heroes defending the Earth from both the Divine Crusaders, and the alien invasion of the Aerogaters. Nobody playable even dies, only losing the two Anti Villains. The problem? The Aerogaters were only one of the fleets of the Balmarian Empire, meaning that the Balmarian Empire might attack again, and even worse, The Guest, aliens that tried to conquer earth by forcing Earth to surrender that caused the Divine Wars in the first place, were not the Balmarian Empire, meaning a second alien menace is out there. Even worse, due to the nature of the Original Generation series, they had only scratched the surface of wars.
Fire Emblem: The Sacred Stones ends up with Eirika and Ephraim defeating the Lord of Terror with the help of their companions, but not before the twins' beloved friend/bitter antagonist Lyon dies in front of them. The last CG of the game has the twins recalling the day they met Lyon. Not to mention the whole issue of Grado falling victim to a catastrophic natural disaster... just as Lyon had predicted and fell into darkness trying to stop. Several charas have to stay behind and help reconstruct the Empire.
In Lufia II: Rise of the Sinistrals, the four Sinistrals are defeated, saving the world from their rule, with the heroes able to withstand one last attack from them in their dying breaths... with the exception of Selan, who soon dies in Maxim's arms. After his companions teleport away, Maxim dies after exhausting his energy to stop Doom Island from crashing into Parcelyte. The game ends with Maxim and Selan's companions celebrating their victory and anticipating the two's return, unaware of (or, depending on interpretation, unwilling to accept) their fate. Made even more bitter by the fact that Maxim and Selan had a son in Parcelyte, who will now live to see his future, thanks to Maxim's sacrifice... but will never know his parents. Averted in the DS version's secret ending. "Jeros, we're home!"
If you don't find the all the pieces of the title artifact in Neverwinter Nights 2: Mask of the Betrayer, you have a choice between staying forever on the Fugue Plane to seal away the Spirit Eater or curing yourself and returning to Faerun, but leaving the Spirit eater free to ravage Rashemen. There's also an additional ending if you got One of Many instead of Okku, and you romance Zafiya. It generally follows the good one, but with one major difference: After you marry Zafiya and return to Faern, One of Many kills her and consumes her soul. In revenge, you hunt him down and eventually kill him as he pleads to spare his life in Zafiya's voice.
If you ignore the stuff that happens after the credits roll in Pokemon Mystery Dungeon Explorers, it's pretty depressing. Your character basically gets erased out of time because the planet didn't go into paralysis (so no one from the future could have come back, including you) and after your companion returns and tells everyone, the last shot you see is them crying on a friend's shoulder at the place you first met, in pretty similar circumstances too. Except he's all grown up. Considering everything you went through, and the fact that this scene takes place a good couple of months after everything's restored, it's pretty jarring.
The first game in the PMD series is equally so. When you and your partner are recovering with your good friends, everyone is happy to have you back with them and that the world is saved... until Gardevoir shows up and informs you that your time in this world is over. The last few shots we have of the Pokémon world before the end credits is of everyone moping over your departure, and your partner sobbing uncontrollably.
Pokémon Mystery Dungeon: Gates to Infinity is no different. The hero is ultimately forced to return home after everything is saved, as it's revealed the prolonged presence of humans in the Pokémon world will cause a distortion that will threaten its existence, plus they're told they'll be forgotten by everyone once they depart, making them decide to leave without telling anybody. Though their friends are made aware of this and manage to give them a fond farewell via a recording, it only serves to make things more painful for the hero; the last shot being of them on their hands and in tears after realizing that they weren't forgotten as they had been led to believe. Most notably, in a contrast from the other games, they don't come back in The Stinger.
X-COM: Terror From The Deep - Defeat the boss alien and you save the world, but the alien city explodes and takes all of your soldiers with it.
It's even worse, because canon dictates that when it exploded, it sent a crapload of pollutants into the atmosphere and basically caused much of the world to need to be abandoned. Nice Job Breaking It, Hero.
The trend for bittersweet endings in continued in Wild ARMs XF, where victory costs the lives of Princess Katrina and King Hrathnir via Heroic Sacrifice to win the day, and Felius is missing and possibly dead after he sacrifices himself to save the world.
Prey ends with Tommy defeating the Mother and destroying the Sphere. However, his grandfather and his girlfriend, the only people he felt any connection with, are both dead. Neither seems terribly bothered by this and her spirit tells Tommy she will be waiting for him, so it's not so bad.
At the end of the final mission in Starcraft, Tassadar sacrifices himself in order to destroy the Zerg Overmind, but Aiur is a smoldering ruin and the central Terran government is led by a monster. The expansion Brood War, on the other hand has an outright Downer Ending.
Brood War also, fairly early in its plot, turns the Bittersweet Ending of the original into a Downer Ending by having a new Overmind be created to rule the Zerg until Kerrigan's rise to power, basically rendering Tassadar's heroic sacrifice ultimately futile in the long run.
The Protoss campaign of Brood War has a bittersweet ending: The Protoss have driven the Zerg from their new homeworld of Shakuras and reunited with their Dark Templar brethren, but Aiur had to be abandoned as a lost cause and Kerrigan used the Protoss' attempts to reclaim Shakuras as a way to eliminate any Zerg who could oppose her.
Starcraft II has this; Kerrigan has been deinfested which has accomplished three feats a.) breaking the Zerg and ensuring that billions of lives will be saved b.) ensuring that Kerrigan can now start working for redemption and c.) humanity no longer has to fear the Zerg. The bad news is that Raynor had to shoot Tychus (his best friend), Mengsk is still in power, and the Dark Voice is still working to jump start the apocalypse; the only difference with his plans is that humanity has a chance to stop him rather than being wholly boned.
At the end of Heart of the Swarm, Kerrigan has finally reconciled her human side with her potential as the Queen of Blades and come to a sort of understanding with Raynor. Arcturus Mengsk is dead, and in addition to settling personal scores this clears the way for the first truly good man to take the reins of power in Terran society in who knows how many decades. She is in complete control of the Swarm, and it will no longer threaten humanity, as she is taking it immediately to do battle with the Dark Voice. Only three things mar the outcome: the massive wreckage that is downtown Korhal, the fact that she still can't be with Raynor, and, oh yes, the bit where the Dark Voice is still planning to invade and destroy everything and they still only have the faintest idea how to fight it, let alone stop it.
Fable II in The Sacrifice route. Sure, the world is saved and everyone has their loved ones back. Except for you. The price for everyone else's happiness was your own because your spouse, children, sister and even your dog is dead. You can never get them back and you have to live with the knowledge that you choose the lives of others over theirs. It doesn't matter what you tell yourself: at the very least, you will miss that dog.
I can't dig up items anymore. I can't complete the archeology quests. I've lost a major gameplay element. NOOOO!!!
Castlevania: Order of Ecclesia, the good ending. Shanoa manages to defeat Dracula and reclaimed her emotions, but in process lost her home and foster brother Albus. And as the said home is evil, she then vanished into obscurity as records of her home became written out of history, probably including herself.
Averting this becomes the main motivation (story-wise at least, completionists be damned) to obtain all 108 stars in most of the Suikoden series.
Rule of Rose: If the good ending is achieved, Jennifer wanders the orphanage making nostalgic comments and then goes to the shed to metaphorically lock the puppy version of her dead dog, Brown, away in her heart forever. The game ends with her leaving as he whimpers.
Metal Gear Solid 2: Sons of Liberty: Raiden stops the terrorists and is reunited with Rose, his girlfriend, but in the process several members of the supporting cast die, he's forced to reconfront his past as a child soldier, and he is left with the words of a psychotic AI, taunting him that everything he has done has gone exactly as planned. Meanwhile, series Big Bad Ocelot is still at large, as are The Patriots, the shadow government that has set up the game's events. If it weren't for series protagonist Snake showing up at the end to offer some words of wisdom and a lead on the Patriots, it would be a downright Downer Ending.
Metal Gear Solid 3: Snake Eater: The good news is that Naked Snake defeats Col. Volgin, destroys the Shagohod, averts a nuclear war and is given a hero's welcome back in the states, but his mentor/mother-figure is forced to take the fall for Volgin's crimes, and it turns out the whole thing was orchestrated by the US Government as a part of its plan to get its hands on the Philosopher's Legacy. Plus, this is Naked Snake's Start of Darkness where he becomes Big Boss, the Big Bad of the first two games.
Metal Gear Solid 4: Guns of the Patriots ends thus, with the Patriots' rule finally ended and the war economy ending, saving the world and humanity. However, although Snake doesn't commit suicide, he will (short of a cure that is never mentioned) die before long of the accelerated aging and shortened lifespan given to him before his birth. On the bright side, Snake himself doesn't seem too bothered by the fact that he's going to die. He has a year to live his life free of outside influences, and in The Stinger, he even sounds happy that he has that chance.
Ace Combat 5 has this, along with Zero and 6: in 5 Chopper was KIA after crashing, your squadron members are declared traitors and officially recorded as being KIA, and while you gain unofficial recognition as the Ghosts of Razgriz, it will be years before the truth about the war and your achievements is known. In Zero you lose both of your wingmen, the first to treason and the second to being shot down by the first. 6 has quite a few: Ludmilla and Toscha are married in a prisoner of war camp, Viktor Voychek is presumably a POW as well (despite giving up the schematics for the Chandelier superweapon), the valiant Ilya Pasternak was KIA covering his squadron's retreat from Gracemeria only for some of them to be shot down in the final battle, Garuda Two's wife and daughter were killed before he could meet them again, and he is confined to a wheelchair after being shot down during the final battle. Oh, and the fate of the Hartman family's husband/father is left unstated.
Zero's Assault Records have what must have been some Bittersweet Endings for some Belkan aces if you shot them down: Robert Gloden Spieler left the Air Force a year after the Belkan War and ended up running a small hotel in San Salvacion by the ocean. (Based on the "FMV" cutscenes taking place at the time of the Usean Continental War in Ace Combat 4, if the same timeframe is assumed for the Assault Records he may have been the unfortunate uncle in that game's cutscenes.) Dietmar Wolf Absender would be tried as a war criminal, although the charges would be dismissed. And Daniel Bierofka Wetterhahn would go from ace pilot to automobile salesman and ordinary citizen.
In Mirror's Edge, by the end of the game Faith's best friend Celeste turns traitor and is helping the CPF hunt down Runners, and may have had a hand in killing her beloved mentor Mercury. On the other hand, she does rescue her sister from Jacknife (by kicking him out of an airborne helicopter!) and temporarily shut down the city's oppressive surveillance servers. Still, both she and Kate are now branded criminals, largely alone and facing down the newly-trained Project Icarus Runner-hunters.
Xenogears ends with the defeat of the evil interstellar weapons system that created mankind to serve as biological parts. Fei and Elly are finally united after many incarnations of tragedy. However, 95%+ of the world's population is dead and civilization eradicated. The most poignant part however is Big Bad Krelian finally achieving his dream of living in a world without war or loss by ascending.
Xenosaga, the spiritual successor to Xenogears ends with the Big Bad defeated and Shion and Allen finally together. In the process, though, we lost chaos, KOS-MOS, and Jin as well as many NPCs and most of the population of the galaxy. The UMN has been destroyed, leaving no method of faster-than-light travel or communication. However, the game ends with a ray of hope as MOMO is working to restore the UMN, Shion and the rest are on a quest for Lost Jerusalem (aka Earth), and a hint that they may find KOS-MOS again.
Freespace 2 ends this way as the Shivans are revealed to be essentially unbeatable due to the magnitude of their warfleets. Upon realizing the futility of further struggle, the GTVA High Command forces a draw, of sorts, by severing all subspace links to Shivan-controlled space. A vital star system (Capella) is lost in the process, along with most of the Terran/Vasudan fleet. It is also heavily implied that the Shivans will eventually find a way around this obstacle.
Halo Wars. The Covenant have been stopped, the Arbiter is dead, the Prophet of Regret has been stopped, and the Spirit of Fire is safe...but then Captain Cutter pauses to lay his hand on Sgt. Forges' empty cryo bay.
Cutter: You got all of us out of there, professor. Anders: Not all of us, Captain.
The Spirit of Fire, left without an FTL Drive, is now effectively stranded in space with no way to reach a human world anytime during the next century.
In A New Beginning, Spyro has rescued Cynder from her enslavement by the Dark Master by beating the curse out of her, and in doing so has delayed the Dark Master's return. However, there are still other ways he can return, Spyro's powers have been sapped by the effort it took to defeat Cynder, and Cynder is worried she doesn't belong after what she has done to the world.
In The Eternal Night, Spyro has managed to defeat the Big Bad, Gaul, but in doing so, he briefly fell prey to dark powers. Now the mountain is collapsing in on him and his friends, with no way out because of Spyro's brief possession and subsequent self-doubt. He has no choice to encompass himself, Cynder, and Sparx in crystal to stay alive. Oh, and the Dark Master has been resurrected, now free to wreak havoc on the world. Damn.
In Dawn of the Dragon, with Malefor's death, the world has begun to break apart. Spyro, with his special powers, manages to save it from doing so. However, Ignitus is dead, and everyone, including Sparx, thinks Spyro and Cynder might be dead too. Made a bit happier at the end when we're shown that Ignitus becomes the next Chronicler and Spyro and Cynder are alive and well, though they still haven't been reunited with their friends.
Morrowind. Sure, you've saved the world from Dagoth Ur, but you've also set into motion the exposure of the Tribunal as false gods, the inevitable fall of the Ministry of Truth, and by destroying the Heart of Lorkhan weakened the metaphysical barriers enough to let the plot of the next game happen...
Oblivion. Sure, you've saved the world from the Oblivion Invasion, Mehrunes Dagon has been banished, and you have become a hero. But, Martin is dead. And since the Empire is left with no Emperor and no heir, the Third Era of Tamriel has effectively ended. Without a leader, the Empire will probably fall. And there is none of the imperial bloodline left to protect the world from another invasion. Which next time will NOT be able to be sealed off or halted as the only person who could turned himself into a stone dragon. So after all that work, all your character did was delay the destruction of the world by a couple of hundred years, which is the blink of an eye to the Daerdra. Sucks to be you.
Skyrim confirms the bittersweet tones of the previous endings. Taking place a few centuries after Oblivion, the Empire has barely reformed, only to be defanged by the Altmer. Morrowind was devastated by the Ministry of Truth's impact and has now been conquered by the vengeful Argonians. In regards of Skyrim itself, when the player finally defeats Alduin his soul is not absorbed like other dragons, it's implied that Alduin will ultimately return to fulfill his destiny as world-eater, and there's no telling if a new Dragonborn will be there to stop him.
Breath of Fire III: Sure, you've defeated the Big Bad and showed her that the world doesn't need a nurse, but one of your best friends is dead and the world will slowly turn into a desert.
In Breath of Fire IV, Ryu sacrifices himself to rid the world of the gods, so that a similar tragedy won't happen again. Although the Mad Scientist Yuna simply claims he can make as many gods as he wants.
The Half-Life series never ends on a completely good note.
In the first game, Gordon is told that his efforts were observed by some extraterrestrial entity for an employment opportunity. He is then given a choice, either join the G-Man (the recruiter/employer), or go against a gross of Xen minions weaponless. Either choice leaves a bitter taste in the player's mouth.
In the expansion pack Opposing Force, the player character Adrian Shepard is sealed for pretty much eternity after the events of the game, since he's never mentioned in the Half-Life universe again...
In Half-Life 2 ends with a massive explosion about to consume Gordon and Alyx. Before it reaches them, the G-man momentarily stops time to rescue Gordon, saying his services will be needed again, while his partner is presumably left to die.
In Episode 2 Eli Vance, Alyx's father, dies in her sight while Combine Advisors suck his brains out after averting a major invasion from the Combine.
The only official Half-Life game that didn't have such a bad ending was Half-Life: Blue Shift, where Barney Calhoun successfully escapes Black Mesa, later appearing in Half-Life 2.
Portal: Chell survived, only to be dragged from the ruins by a robot, presumably to undergo yet another round of 'testing' in Portal 2.
Portal 2 has GLaDOS deciding that she's tired of dealing with Chell and releasing her to the surface, along with her Companion Cube (which apparently survived incineration). Of course, this is several hundred years into the future and GLaDOS implies there's something unpleasant outside, alluding that the Combine might just still be around. Chell has also just expelled Wheatley, her only other friend into space, and she has effectively traded his freedom for her own.
Star Fox Command's nine endings included several bittersweet ones, most of which included Krystal abandoning Star Fox to join Star Wolf, her relationship problems with Fox unresolved. The most gut-wrenching of them involves Krystal saving the universe with Star Wolf, only to be shunned by the public for her double-crossing of Star Fox, leading her to leave and wonder alone, becoming a bounty hunter known as Kursed. The most bitter sting is that years later she comes across Fox, who does not recognize her. Other slightly more upbeat, yet still somewhat sad endings involve Peppy and his daughter reminiscing about their dead/wife mother while Fox and Krystal patch things up, Slippy retiring with his fiancee and years later telling tales about Star Fox while wondering if they were still out there, and one ending where Falco, depressed at not being able to rejoin Star Fox in time to rescue the universe, is convinced by Katt Monroe to start his own team called Star Falco. A variant on this ending has Fox and Falco both being depressed after Star Wolf beats them to the final boss, and they cope with it by dropping out to become G-Zero (an F-Zero reference) racers.
Knights in the Nightmare in its "good ending". Despite beating the Big Bad, the loyal knights of King Willimgard are all dead, his son is dead, the Tiamat race is doomed, and the whole kingdom is in ruins.
Every single ending aside from the ones that are Nonstandard Game Overs or just plain nightmarish is like this:
If you found Ancardia and won the final battle, Willimgard gets to come back to life, but the world is still a mess. He may or may not get his Tiamat lover back as a farewell present, and poor Maria gets damned and thrown out of Asgard despite how hard she fought to fix her mistakes as Marietta.
In Meria's route, it's even worse, as the only way to get a reasonably "good" ending is to backstab Meria and side with Marietta despite everything you've been through together and the self-destructive loyalty she's shown you.
And if you decide that protecting your True Companions is more important to you than textbook order, then win your battle against Marietta, Meria becomes Melod Melgis. The good news is that there's no more corrupt Asgard and no more Hector. The bad news is that the world kind of sucks now.
Every saga in Disciples 2: Dark Prophecy has a Bittersweet Ending. Even the bad guys don't get everything they want in the end. Empire: Demon Uther was defeated, but not before he murdered his father the Emperor, leaving the Empire in ruins without a ruler or an heir. Undead: Mortis succeeds in reviving her lover, but he is so repulsed by what she had become and by what she had done to bring him back that he rejects her and abandons her forever. Legion of the Damned: Demon Uther wasn't actually their god reborn; he was a Creepy Child draining his power. The loyalist Legions manage to kill him, but their god Bethrezen is still sealed away, so they have to go back into hiding. Nobody in this game gets a completely happy ending.
The normal ending of Tales of Symphonia: Dawn of the New World. The world is saved, but Ratatosk, and by extension, Emil, has to seal himself away for 1000 years so he can repair the Mana flow. At least he'll have Richter and the Centurions (including Tenebrae and Aqua) to keep him company. If the right choices are made, an after-credits stinger reveals Ratatosk seperated Emil from himself so he may be with Marta. Doesn't change the fact Ratatosk, Richter, and the Centurions are sealed away for 1000 years.
Frontlines: Fuel of War: You just fought through the downtown core of Moscow and held a square against a seemingly endless supply of Reds. Too bad the Chinese are still in the fight, and that citizen militias and the harsh Russian winter are likely to beat you back.
The second game, both chronologically speaking and in order of release, Kingdom Hearts: Chain Of Memories has two endings, one for Sora-mode and one for Riku-mode, and neither are all that cheerful: Sora ends up a shell of his former self, having completely forgotten Kairi, and must sleep for a year while Namine restores his mind to how it should be—that not sad to you? How about I tell you that Namine, under orders from the Big Bad, was the one who replaced Kairi in Sora's memories with herself, and now must make Sora forget she ever existed when he was the only person in her life who actually cared about her. As for Riku, it turns out that Ansem has been possessing him and while he stops him now, he'll always be lurking, waiting to possess him again, and that no matter what he will have to come to terms with his own darkness. He finally finds Sora again — but just after Sora begins that year-long sleep, and thus has to leave him while he goes on his own path.
Fourth game released and a complicated sort of Prequel / Interquel/whateverquel mix, spanning from just before the end of the first game, over the events of the second, and ending right before the third, Kingdom Hearts 358/2 Days ends with the "villain"protagonist running to the cessation of his existence as a separate entity that will occur in the prologue of the third game, after having had to do in his poor friend who was Doomed by Canon, setting up most of Kingdom Hearts II.
Then there's Birth By Sleep, which is not bittersweet...it's a flat out downer.
Kingdom Hearts: Coded, released for cell phones in Japan and later remade for the DS for the US, doesn't have a happy, bittersweet, or sad ending. It instead ends on a pure Sequel Hook.
Kingdom Hearts: 3DS Dream Drop Distance ends with the characters doing juuust better than breaking even, with the Big Bad still at large and stronger than ever and, of the two protagonists who set out to get the Mark of Mastery, only one succceeded, while the other almost died and needs to retrain from square one.
A possible ending to Mass Effect 2 is that the Collectors have been stopped, and the Normandy escapes the Galactic Core, but at the cost of Commander Shepard, his team and the Normandy's crew, aside from Joker. And the Reapers are still going to invade, with no-one left to stop them. This ending isn't canon, though, as the canonical ending has Shepard and at least two of the team left to defend the galaxy.
Any ending other than the Golden Ending is going to be bittersweet, as well, and they can be imported. You could, for instance have Shepard survive, but lose the Normandy crew and all but two of your squadmates in the process, possibly including Shepard's love interest. Sucks to be you, Shep.
Even the Golden Ending is bittersweet. You've killed the Collectors, but hundreds of the most powerful star-battleships ever devised are coming to wipe out all advanced life in the galaxy:
Harbinger: Human. You have changed nothing.
Factor in Arrival, where the Reapers invasion is halted, but at the cost of 300,000 lives.
Discounting the other eight potential endings, even if you did absolutely everything, complete with 100% Heroism Rating and 100% Completion, Mass Effect 3 gives you three final options on how to deal with the Reapers. These are given to you by The Catalyst, the controlling intelligence behind the Reapers, which lives in/as the Citadel.
"Control", in which Shepard transcends beyond his/her mortal coil and supplants the Catalyst as a more hands-on controller of the Reapers, rebuilding and tending to the galaxy at large... but leaving behind all his/her companions due to his/her vastly expanded consciousness.
"Destruction", in which Shepard destroys The Catalyst, sending out a wave that will destroy all synthetics in the galaxy. The Reapers, as well as the Geth and EDI will die, and galactic civilization will have to rebuild on its own. However, this is the only ending where Shepard seems to survive, if the Effective Military Strength rating is high enough.
"Synthesis", the third option, in which Shepard sacrifices himself to introduce his DNA to the Crucible, sending out a wave through the Mass Relay network that transforms all life, both synthetic and organic, into hybrids of the two. Changed and with their reason for invasion gone, the Reapers retreat.
In all three options, galactic life is pretty much guaranteed to take a hit, but as the Distant Finale shows, life will go on and the races of the galaxy will recover.
The Extended Cut brings in a fourth ending, in which you effectively tell the Catalyst "screw you" and do nothing. This results in the Reapers winning and destroying you, all your friends, and all galactic life... but a light is flung into the future and The Stinger reveals that the next generation beat the Reapers permanently.
By the end of The Darkness, you've successfully killed Paulie and Shrote. But Jenny is dead, and at the cost of your soul belonging to The Darkness forever. And you're allowed one last meeting with Jenny, before you're seperated from her forever. The sequel has Jackie tearing his way through hell to find Jenny and finally finding her after two years of guilt and depression, only for Jenny to become the host of the Angelus and abandon Jackie and the Darkness to hell.
The good ending for the "Trouble on the Homefront" quest. Vault 101's tyrannical Overseer steps down in favor of Amata and the Vault is finally opened to the rest of the Wasteland, but Amata is forced to permamently exile you from the Vault because most of the Vault's residents still believe it's your fault the situation got as bad as it did. At least she gives you a nice parting gift.
The good ending for the vanilla campaign isn't without a bitter taste either. Even if you do survive the obscenely high radiation you got by activating the purifier (which you can only do with Broken Steel installed), it doesn't change the fact that your father, whom you were trying to find for the whole game, died to protect the purifier from the Enclave.
Almost inevitable in Dragon Age: Origins, depending on the decisions made throughout the game. The only way to defeat the archdemon without requiring a Heroic Sacrifice from someone is to allow Morrigan to perform a blood magic ritual that will let her conceive a child with the soul and power of an old god - with no guarantees as to what consequences this might have for the world as the child grows up. If this ritual is not performed, either the Player Character will die, Alistair will die, or Loghain will die and Alistair's faith in the PC will be so thoroughly broken that he will leave in disgust.
The ending is especially gloomy if you romanced Alistair and refused Morrigan's offer. Rather than let the woman he loves die, Alistair kills the archdemon and dies instead. You've ended the blight and saved Ferelden, but it's unlikely you'll be in any mood to celebrate.
Also, Denerim and Lothering have been sacked and all but decimated, as are the Grey Wardens (their numbers being from three to one depending on your choices with Landsmeet and the Dark Ritual). Countless number of citizens have either died or fled the country, the corruption of the Blight has made a large portion of the country barren and unsuitable to live, and depending on your choices Ferelden has lost one of its greatest generals if you decided to execute Loghain instead of recruiting him, and the new king hasn't got the slightest idea on how to rule a country, though epilogue dictates that Alistair will either become a good or a great king in time depending on if he's hardened.
In MySims Agents. No, really. After getting the Nightmare Crown back, Morcubus suddenly comes in and takes it and is about to open the portal to the Nightmare Realm when Evelyn suddenly comes in and stops him... by sucking them both into the Nightmare Realm. And she had just been reunited with her father. Ouch. And wait, there's more! If you complete all of the dispatch missions, you'll be able to go and save Evelyn. But to save Evelyn, you have to save Morcubus. And when you do, he escapes. Great.
In Wrath of the Lich King: Arthas has been defeated, and the scourge has been destroyed, but many soldiers died, and Bolvar gives up his chance at humanity to contain the scourge. The Horde in particular had hoped to rescue Bolvar so they could try and smooth out some of the issues stemming from the Wrathgate.
Another WoW: WoTLK questline has a spirit animal, Ursoc, become corrupted by a failed attempt to grow another Worldtree. The quest ending leads to Ursoc's death, his subsequent release from Vordrassil's taint as well as the corruption being lifted from the general area. Ursoc thanks you, his spirit finds rest, and Vordrassil can't corrupt any more of the environment... but unfortunately, when you return, the druid that set you on the quest only stares blankly at you with a broken mind (either due to the corruption, or because of lazy writing).
BioShock 2. The good ending ends with you dying, but Eleanor Lamb and the rescued Little Sisters are now safe on the surface. Eleanor takes your conscience and puts it in her body, allowing you to live on inside her. It gets REALLY bad when you add in the facts Sinclair is dead, Mark Meltzer became a Big Daddy ironically assigned to protect his daughter, Gil Alexander is either incredibly mutated and insane or dead, and Rapture is still fucked up, with only the fate of Eleanor and the Little Sisters being definitely good, you can only imagine how bad the "bad" ending must be.
BioShock Infinite: Booker learns that he and Comstock are one in the same, Comstock being an alternate version of Booker that accepted baptism to cleanse himself of past sins, only to found Columbia (which turns out to be a flying fortress disguised as a flying city) and eventually destroy America. Ergo, the only way to prevent Comstock from ever being born is for Booker to die, himself. Thus, he lets Elizabeth and her alternate versions drown him, thus killing every version of Booker that would've become Comstock.
The final cases of the first three Ace Attorney games kinda end like this. Phoenix exposes the real killer and wins the day, but either his client or another suspect he was desperate to exonerate still end up imprisoned for lying under oath and interfering with a crime scene. The third game is even worse, as Godot will also have to stand trial for his crime (assuming he even lives that long), and Maya witnessed her own mother's death but has to put on a strong face for Pearl's benefit.
Digimon World ends with Hiro still in the Digital World. He's saved that dimension from total destruction at the cost of never being able to return to the human world. Mind you, he was also taken into the Digital World against his free will in the first place by some cosmic force, so this is also a case of Being Good Sucks. And since it was such a random teleportation, his parents will come home and find him gone forever with no explanation or note explaining anything.
None of the endings of Devil Survivor are 100% happy. Yuzu's ending is a straight up Shoot the Shaggy DogDowner Ending, but the rest are varying degrees of this. No matter how hard you try, everything inside the Yamamote line is more or less destroyed and hundreds of people die. The government will cover up the events of the game and God's next ordeal is inevitable unless you pick the Chaos ending (which allows the demons to overrun Earth) or the Law ending (which implies the protagonist went Knight Templar with the power). The Updated Re-release for 3DS extends the endings, and most of them either bring the story to an end full circle or fix any damage done by the game's choices.
The ending of DonPachi, in which the player character joins the elite Super Soldier force DonPachi Squadron...after having completed training in which he is ordered to kill a massive plurality of allies posing as enemies.
"In the end, we were not the ones who made this 'mission' a success, it was the numerous soldiers who lost their lives that contributed to the creation of these super soldiers. Thus came about the elite combat force, 'DonPachi'."
Red Dead Redemption. Sure, Jack gets revenge for John's murder, but that doesn't change the fact that the man he grew to admire and sympathize with is dead. Furthermore, Jack has become a wandering gunslinger and a broken shell of a man, exactly what his father didn't want for him.
Both ActRaiser games have such an ending. In the first, The Master succeeds in killing SatanTanzra, resurrecting the world, and banishing evil... and the people decide they don't need him anymore, and just turn their backs. The second borders on an outright Downer Ending. The Master defeats Tanzra once and for all, freeing the world from evil. Unfortunately, not only do the people dump you again, but your Sky Palace is destroyed, all your angels are dead, and you're more or less trapped in Death Heim. The last shot of the game is your statue being overgrown with plants and crumbling to dust.
The Baldur's Gate Series has a few bittersweet endings for some of the NPCs. Each spoiler contains the epilogue for each NPC:
Aerie: "Aerie - Normal Epilogue: Aerie continued adventuring years after leaving my company, often traveling with a larger group but sometimes striking out on her own to use her considerable power to fight against slavery in the Realms. Her compassion grew tainted by revenge, however; revenge for what had been taken from her when she was in chains and could never be restored. She might have lost herself to her vengeance entirely had fortune not smiled upon her. The tale goes that Aerie, filled with a righteous fury, destroyed a slaver enclave in the northern hills of Cormyr single-handedly. She was surprised to find a group of avariel elves that had been held captive there and quickly freed them, and was in turn invited to return to her long-lost home of Faenya-Dail. She learned much while she was there. Most importantly, she learned she was no longer truly one of avariel, and let go forever of the wings that she had lost. Faenya-Dail was no longer her home, and it was with mixed emotions that she bid it farewell. It is said that Aerie eventually became a high priestess in Understone, a gnomish village her mentor Quayle had sometimes spoken of. He had been her true family, and it was among his people that she finally found happiness and the family she had always longed for. It was also said that Aerie prayed for me, each night as the stars revealed themselves in the sky above. She sincerely hoped I had been fortunate enough to find the peace that she had...for without me, it would never have been possible."
Anomen: "Anomen – Normal Epilogue: Eventually parting ways with his companions, Anomen would enter the hierarchy of Helm's church, over time rising to the rank of High Watcher. He remained restless and dissatisfied, remembering his days adventuring with <CHARNAME>...and though many friends would urge him otherwise, Anomen never felt that the church was his true home. He remained in his position for a year until finally he could bear it no more. He left active duty in the church and, for a time, wandered the new land of Maztica as a missionary. Anomen remained a troubled soul, still never content even though his prowess earned him great respect from the new friends he encountered. When the powerful evil priest Yamash summoned a horde of demons in an effort to rid Maztica of all life, Anomen would at last find his purpose. He alone was responsible for organizing the tattered remnants of the Amnish soldiers and local Mazticans into a united army that stood against the dark priest. In the great battle that followed, Anomen was seen plainly by all to plunge into combat single-handedly against Yamash. He did not have <CHARNAME> or other companions beside him: alone he stood against the tide of evil, and for once he was not found wanting. He was last seen from afar, shedding tears of joy as he engaged Yamash and shouted out to Helm while chanelling a blinding flash of power. When it cleared, both the priest and Anomen were gone. The battle was won and Maztica was saved. Anomen would forever after be regarded as a hero, inspiring the creation of a protective order of knights in his name. A new order for a new land."
Cernd: "Cernd Epilogue: Cernd left the adventuring life to return to his grove in Tethyr, promising to take up his responsibility and raise his son, Ahsdale, as he believed a father should. Cernd would eventually become the Grand Druid and make a name for himself throughout the realms by not only fighting for the balance of his grove but in protecting the sanctity of life in all realms and in all peoples. Cernd would discover in time, to his regret, that in his attention to his duty he had forgotten his promise to Ahsdale. His son had left the grove long before and Cernd learned that Ahsdale had become an evil and twisted wizard in command of a power that threatened the Sword Coast. Determined that this was his burden alone to face, Cernd solemnly abdicated as Grand Druid and sought out his son. He engaged in many battles with the forces of his son, wielding the forces of nature with a great fierceness that would be regarded as legendary by all who saw it. Cernd finally confronted Ahsdale himself deep in the Forest of Tethyr, and made a final effort to convince him to turn away from his path. Ahsdale refused, and Cernd fought his only son in a long and terrible battle that eventually saw both of their deaths. With his last breath, Cernd would crawl along the ground to clasp Ahsdale's dead hand, tears flowing down his face as he begged his son's forgiveness. Cernd's spirit would enter that of a great oak within the forest, and it is believed that this immortal oak still stands, and that around it has grown a wondrous grove of great beauty that is home to the rarest of the Realm's magical creatures. Each fall the great oak and the grove around it would turn the grimmest shade of red, a reminder that even the most flawed amongst us may eventually find their balance."
Jaheira: "Jaheira – Normal Epilogue: The events of the Bhaalspawn saga affected Jaheira deeply. It was her duty to protect the greater balance of things, but in the years to come she found an increased portion of that fight occurring within her own mind. Witness to great change while in <CHARNAME>'s company, she had become acutely aware of how fleeting life was, and how the loss of those she held dear ate away at her thoughts. In time she would be known as a tireless champion of balance, one that sometimes acted in concert with the Harpers and sometimes did not. Jaheira operated quietly, appearing when needed and moving on when not. Many called out to her for leadership, but always Jaheira would deny that she was capable of such and say that there was somewhere else that needed her aid more. She remained distant and guarded, never staying long in any one place. It is said that she crossed the Forgotten Realms thrice over, always wandering and always searching...until finally she began to wonder what it was, in truth, that she was searching for. What happened to Jaheira later in life is not well-known. Some say that Elminster eventually came to her and convinced her to take her place amongst the greatest commanders of the mysterious Harpers. Some say that she fell in battle against a great lich that threatened to defile the northern forests. Some also say that she went in search of <CHARNAME>, traveling to lands far beyond our own. Whatever happened to her, Jaheira never did return to either the Sword Coast or Tethyr ever again."
Keldorn: "Keldorn Epilogue: Keldorn Firecam thought his travels with <CHARNAME> marked the end of his active career, both as an adventurer and in service to the Order. He retired to Athkatla, hoping to live in as much peace as an old warrior can expect, but the call to serve came one last time. It was years later, and Amn was besieged by giants. In his 60th winter, Keldorn and five knights held a strategic pass until the main Amnish force could arrive. He won the day, but his wounds were severe and the old paladin fell on the battlefield. As his knights watched, the hand of Torm descended upon the scene, and when it departed, Keldorn was gone. From that day, visions of the True God were accompanied by the stalwart ghostly form of Keldorn at his right hand."
Sarevok: "Sarevok Epilogue: In the years following his resurrection by my hand, Sarevok spent many years wandering throughout the Forgotten Realms, rarely spending much time in any single place. In Berdusk, he is said to have routed an army of invading orcs, displaying such fearsome power and rage that terrified locals weren't sure whom to fear more... only to disappear quietly without expecting a reward. In Westgate, he arrived as conqueror, brutally enforcing his will over the city only to mysteriously vanish months later, leaving his own startled men to the mercies of the angry mobs. He acted like a man that did not know himself, and all the stories agreed that Sarevok was a tortured soul, balanced between life and death, never to achieve either. Those who knew Sarevok best, which were few, said that the tormented warrior would in turn curse me for giving him his second chance...and then thank me. Eventually he disappeared entirely from the Realms, said to have assaulted the Abyss itself or even taken his own life. In truth, he journeyed to Kara-Tur to bury his one true love, the warrior Tamoko. He never returned, though the stories endure."
Viconia: "Viconia – Normal Epilogue: Viconia traveled only for a short time after parting ways with <CHARNAME>, eventually starting a cult dedicated to Shar within the massive city of Waterdeep. One of her followers would eventually turn against her, precipitating a furious Viconia to slaughter the entire cult, herself. Shar did not forgive Viconia this trespass and removed her abilities. Viconia stubbornly refused to atone, however, and instead left Waterdeep to wander the Realms. The dark elf became known as an enigmatic and powerful figure as tales of her spread...and while it was known she no longer worshipped Shar, it was also known that her clerical powers were still great. Who the dark lady now worshipped, however, was her own secret to keep. She reportedly raised an army against the Vaasan Witch-King, viciously attempting to subvert rule over his Kingdom and only barely being defeated after several military failures. Viconia prevented an attempt by the Knights of the Shield to take over Calimport...only to take over the city herself days later and institute a reign of terror and cruelty which is spoken of even years later in shuddered tones. Viconia abandoned Calimport and, it is said, returned to the Underdark from whence she came. Hers was not a gentle return, however, as Viconia would become a conquering force amongst the drow to give even Lolth pause. Her mettle had been tested by both worlds, Viconia said, and proven herself worthy. She would make the drow strong whereas now they were weak. What eventually became of Viconia is unknown and shrouded in rumor...but it is said that even the great Spider Queen does not rest easily any more."
Viconia: "Viconia – Romance Epilogue: Viconia and <CHARNAME> continued their adventuring careers for several years, gaining considerable fame after being drawn into central roles in two wars that rocked the Sword Coast. <CHARNAME>'s standing in the Realms grew considerably over time, his dark maiden always at his side. Eventually, Viconia became pregnant with <CHARNAME>'s child, an event that caused much argument and strife between the couple, resulting briefly in their seperation. The birth of <CHARNAME>'s son, however, would change Viconia forever. She would return to <CHARNAME> and convince him to settle finally in Baldur's Gate, dedicating herself utterly to raising their son and teaching him the ways of the drow as well as the ways of <CHARNAME>'s people and marvelling at the power the boy already was demonstrating. Though she delighted at the understanding in her son's eyes, she would not live to see him grow. Viconia was a powerful priestess and all but immune to common poisons, but the venom of the Spider Queen's vengeance was not easily resisted and her reach is far. Poisoned by a servant of the goddess Lolth, <CHARNAME> railed in rage as even the most powerful magics proved ineffective in curing his ailing wife. Viconia's last words were whispered to <CHARNAME>, in private, before she finally succumbed and are unknown...but the tale is well-told of how <CHARNAME> held the body of his dark maiden close to him and wept, while the entire city wept with him, suffering a loss of something precious that they never even truly knew they had. The furious <CHARNAME> left Baldur's Gate and raised his son in secret far away. Tales vary of him, some saying he began a crusade against the drow in the Underdark, some claiming he became a hero in the far-off northlands...and some even saying with surety that <CHARNAME> had waged war against Lolth herself in the abyssal Demonweb Pits...but all agreeing that the former son of Bhaal had been changed forever by his love for the dark maiden. As for the son, tutored by two of the most potent beings in the Realms? He would go on to forge a legend that would rival that of his father. That, however, is a different story..."
In the game series Lost in Blue, one of the possible endings usually requires going through 365 days on the island without finding a way off. Suddenly there's a cut scene where the characters realize that they'll never get off this island, but it doesn't really bother them anymore.
Dragon Quest III ends with your hero defeating Zoma and saving both worlds — but the link between both worlds is sundered, stranding them in the former dark realm along with whatever friends they brought to the final battle. While recognized as their savior and raised into legend, they can never return home, leaving their mother to wonder what happened to her only child just like Ortega did. In some remakes, you can allay this a little by resurrecting Ortega after his death, at which point he reunites with his wife and chooses to stay with her rather than make another attempt to kill Zoma himself, but that doesn't solve the issue of the hero being stranded.
Dragon Quest VI has a similar ending to III, only with the Real World and the Dream World replacing the two worlds of that game and with Mortamor replacing Zoma. However, the bitterness of the ending is compounded by the fact that Ashlynn, who is not an inhabitant of the Real World, is trapped in the Dream World forever.
Dragon Quest IX actually can be viewed as a genuinely happy ending for its main quest. Unless you think that the Hero would not be happy as an immortal trying to protect an entire world from evil while their family has gone to live with "The Almighty" and all mortals have completely forgotten all the Hero's actions as their Guardian. The mini arcs, on the other hand, have a lot of these.
Coffinwell: With your help, Dr. Phelming was able to seal the sentient disease that placed a death curse on the town, but not in time to save his beloved wife. On the plus side, the whole incident causes the originally Jerk Ass doctor to man up and actually work for the benefit of his town.
Porth Llaffan: It turns out that the Lleviathan, who the townsfolk had come to rely on to the point they all became lazy, was actually the spirit of young Jona's dead father. After a tearful farewell, Jonas' father ascends to heaven, and while Jona and the townsfolk resolve to work hard again, it's hard to forget just how dependent they were on Lleviathan. Oh, and the whole incident sends the mayor into an Angst Coma that he doesn't recover from until you complete a sidequest available much later on.
Bloomingdale: You learn that the rich young girl who had mysteriously recovered from her crippling disease really did die and her doll became sentient and took her place. After the spirit of the girl rescinds her wish, the doll returns to being a doll to sit at the gravestone of her only friend for eternity, as she has no soul to travel to the afterlife with her. Biggest Tear Jerker in the game.
Metroid Prime - The corruption has stopped spreading on Tallon IV, but Samus' actions have created Dark Samus. She also mourns the destruction of the Chozo Temple, which was their last great work. The game ends with her just sadly staring at the smoking ruins of it.
Echoes - Samus has destroyed Dark Aether, but Dark Samus is still about and causing havoc. Also, the Ing have already wiped out the GF Marines and a large portion of the Luminoth population.
Corruption - Samus has finally defeated Dark Samus and destroyed all Phazon but, in the process, had to kill three of her friends and fellow bounty hunters.
Super Metroid - Samus has killed Mother Brain, but has lost the closest thing she has yet had to a child, as well as her childhood home in the process.
Metroid: Other M - The Bottle Ship and its evil (or misunderstood) AI are destroyed, but at the cost of the lives of Adam and most of his men. And the people who made this bioweapons lab mostly get away with it.
Metroid: Fusion - Samus has destroyed the X parasite, by blowing up a space station and the planet it orbited, but openly admits she's probably a fugitive for destroying federation property.
Mitsumete Knight: depending on how well you fared in Level Up & Medals-wise, and in your relationships with the girls you met during the story, you can get Knighted as a Holy Knight (the most prestigious title of the country you're fighting for as a foreign mercenary), and recieve the confession of love of one of the girls (and maybe even one from the Princess of the country)... But no matter what, after you win the war for the country, the ungrateful rulers of said country will pass a bill enforcing the expulsion of all foreigners, which means you're included in the lot, and neither the (puppet) king nor the aforemented princess can do anything about it. And if you scored a girl, while most of them will follow you, two of them won't be able to, one being too young, and the other too ill, so the only thing you can do for those two is to make a promise to meet again a few years later when they'll be older / healed, which is actually rather heartwarming.
The first is that, after you lost all of your childhood friends — Yuri, Adele, and Clive — you make good on the promise you made to Clive to take care of Rosaly, your adopted sister, and the ending is that she gave birth to your child.
The second is that, provided Clive lives, he will have a family with Rosaly, with you becoming a wandering, nameless adventurer.
The third is that you become bodyguard to Queen Adele. Despite this, she publicly renounced her intent on marrying, since offspring will only breed violence due to inheritance and Succession Crisis (a big, big part of the story in fact) and thus will remain without spouse. Adele does however, sneak a deep kiss outside the public eye with you, and while the epilogue says that she never took a consort or bore any child, you are described to be the closest she has to a husband.
The fourth ending has you become the King, presumably of Natra. You ruled with an iron fist like a despot, and later in your reign, get assassinated. The bittersweet part comes that this ending is possible if you select "I want to be the King" when Nicola asks you about your dream early in your childhood intro chapter.
While the original Chrono Trigger ends on a positive note, an additional FMV is shown at the end of the PSX and DS versions. In this scene, the player is shown a city under siege and some soldiers fighting: one of these, a city guard, ultimately falls with the legendary Masamune on his hands. You can assume that this city is Guardia — Marle, Crono, and Lucca's home, thus leading into the events of the sequel.
Even worse, the DS version has an optional bonus dungeon in which you can fight Dalton, the Zeal Army captain that previously served essentially as a comical character. By defeating him, you will learn that he's responsible for the Fall of Guardia.
In the DS version you can fight an optional Bonus Boss who is none other than the primitive form of Chrono Cross' final boss. If you defeat it, you will unlock the 13th ending, that is practically a Downer Ending. In the "canonical" ending, the heroes defeat Lavos, which is sent into a Reality-Breaking Paradox dimension. Here it merges with Schala, Magus's sister, creating the Dream Devourer. The player can travel to this dimension and fight the abomination with the help of an alternate-timeline Magus. At the end of the fight, Schala sends the heroes back to their dimension, and the Dream Devourer (who is still alive) begins to turn into the Time Devourer — Chrono Cross' final boss. The alternate-timeline Magus is then stripped of his memories and left wandering in a forest, thus implying that the character Guile that can be recruited in Chrono Cross is Magus himself.
Target Earth features the protagonist Rex fighting to save Earth and her colonies from an unknown assailant. Throughout the course of the game, Rex learns that the enemy are a group of cyborg humans who traveled into the outer reaches of space as pioneers. He begins to sympathize with them once he learns that they ran into severe problems but their cries for help went unanswered. The reason was that Earth had undergone an apocalyptic world war and had to rebuild from the ground up; they were in no shape to send help, even if they did receive the transmission. Rex keeps fighting the good fight, but by the time he kills The Dragon, all he can say is "Another good man dead." Once he defeats the Big Bad, he sets his Assault Suit to self-destruct and symbolically walks away from it.
The Ultima series ends this way. When all is said and done, the Avatar and his companions manage to save Brittania one last time (hopefully for good) by finally defeating the Guardian. Sadly, the Avatar must perform a Heroic Sacrifice to do so because the Guardian is the manifestation of everything the Avatar cast aside after performing the Quest to become the Avatar of Virtue — as long as the Avatar lives, the Guardian will too.
Cave Story's normal ending is one of these. Quote, Sue, Kazuma, Itoh, Momorin, and possibly a couple others escape, but the other half of the cast dies, the Mimigas are almost certainly extinct, and it's hinted at that not even the Colony Drop would stop the cycle of the Demon Crown.
In ending A, Nier defeats the Shadowlord and rescues Yonah, finally ensuring her survival after a five year struggle, but the world is still a slowly dying husk, Facade is in ruins and without a king, Emil (seemingly) died in a Heroic Sacrifice, Weiss fades from existence after losing its power, and Kainé, despite her feelings for Nier, has to leave them to attend to "unfinished business".
In ending B, not only does all of the above happen, but the Shadowlord, and the Shades in general, are given the mother of all Alas, Poor Villain moments. On the plus side, The Stinger shows that Emil is still alive...as a disembodied head. To his credit, he doesn't seem to mind all that much.
In ending C, Nier is forced to kill Kainé to prevent her turning into a Shade. Kainé finally has the peace she longed for, and Nier finally realises he loves her, but now he's lost his one remaining companion.
Company of Heroes ends with Able Company leading the encirclement of the Falaise Pocket, capturing a crippling percentage of the Wehrmacht. On the other hand, Captain Mackay is dead and 80% of Able Company is either killed or wounded. War Is Hell, indeed.
Both expansion packs actually make things worse. Not only are most named characters ultimately killed by the end, in an indirect way, YOU kill them off when you play the same scenario but from a different point of view.
In Tales of Valor, one scenario has you, the Germans, defending a town to keep the Falaise Pocket open. The same Falaise Pocket you, as the Allies, closed in the original game, effectively making Tales of Valor a doomed ending.
Again in Tales of Valor, another scenario has you, the Allies capturing a town. At the end of the scenario, you learn that the last surviving named character later went on to take part and was killed in Operation Market Garden. But in the other expansion pack, Opposing Fronts, you play as the Germans who ultimately succeed in defeating the Allies in Operation Market Garden.
Lunar: Eternal Blue "officially" ends with Zophar defeated and Lunar safe, but Lucia is forced to return to the Blue Star, leaving Hiro behind on Lunar. The epilogue allows you to find Hiro a way to travel to the Blue Star, but this only sets up another bittersweet ending: Hiro is able to be with Lucia but at the cost of leaving his friends and family on Lunar, probably forever.
At the end of Advance, Mike's thought dead best friend Vinnie is revealed to have faked his death in order to get away with the entirety of the money the two had heisted. Mike kills Vinnie and gets back the money, but nearly every major gang in Liberty City is out for his blood, and his only true friend, Eight Ball, has been arrested. (Fortunately, those who've played Grant Theft Auto 3 know that he eventually escapes.)
Chinatown Wars ends with Huang, after a harrowing journey throughout the city, finally avenging the death of his father, retrieving the stolen ancestral sword, and becoming the new leader of the Liberty City Triads. On the downside, a lot of people, many of them Huang's friends and allies, died along the way.
The Revenge ending of IV. Niko finally kills Big Bad Dimitri and finally finds some measure of peace in his life, only to see his girlfriend gunned down by Dimetri's vengeful dragon. Despite this loss, Niko is still able to come to some form of peace after avenging his girlfriend (who was kind of a bitch anyways), his cousin Roman is alive and well (the Deal ending would've had him killed instead of Kate) and is in fact soon to be a father, which is a major step up from the Butt Monkey status he had throughout the game.
The Ballad of Gay Tony ends with Luis nearly killing Tony. They both survive and get out of debt, although they lose the diamonds nearly every gangster in Liberty City had been fighting over. Unlike the main game, however, this is far further on the sweet end of the Bittersweet Ending spectrum.
Tales of Rebirth: the world is saved, and Agarte can finally tell Milhaust her feelings, but suddenly she collapses and dies in Milhaust's arms. Then he realizes that he loves her too, but then again too late...
Star Ocean: The Second Story/Second Evolution. The planet of Expel is saved, the Sorcery Globe is dealt with, and most of the heroes can go back home. But at what cost? Remember Narl/Nall, Mirage, Marianna, Noel, and Chisato (if you didn't recruit them), the psynards, the buzzing Fun City, the wondrous technology, and all the random townspeople you ran into during the second half of the game? They're gone forever, and nobody other than the heroes realises that they ever existed.
The ending of Deadly Premonition definitely counts. The murderer behind Greenvale's killings, as well as the manipulator behind all the other red seed murders are discovered and defeated and Zach is freed from the Red Room, but Emily and Thomas are both dead.
These are pretty much the standard for the Thief series. In Thief: The Dark Project, Garrett loses his eye, but ends up saving the world from The Trickster. Nevertheless, his accomplishment goes completely unnoticed and uncared for by pretty much everyone. In Thief II: The Metal Age, Garrett saves The City again and possibly the world from Karras and the Mechanists. Not only does the achievement go unnoticed by The City, he loses the Pagan wood nymph, Viktoria, his one true romantic interest, in the process. The kicker? He didn't realize how deeply he cared about her until it was too late, and is informed that her loss was supposed to happen.
Mortal Kombat 9. Raiden succeeded in fulfilling his future self's warning to prevent Armageddon, but in process, the majority of the Forces of Good ended up killed, leaving only him, Johnny Cage, and Sonya Blade as the remnants of the Forces of Good (and occasionally Scorpion, depending where his moods swing). On the other hand, the Forces of Evil only lost Shao Kahn, and then there's still Quan Chi planning to initiate the return of Shinnok perMortal Kombat 4. Even worse, Liu Kang, long considered The Hero of MK, dies firmly believing Raiden, his formerly beloved mentor, betrayed him and all of Earth Realm.
The best ending of the Kongregate flash game Immor Tall. The alien saves the human family it befriended but succumbs to its wounds and dies in the end. The family briefly mourn the death of their new friend before fleeing the scene, and snow slowly buries the alien.
Breath of Death VII. The undead heroes save the last human alive and return the crystals to him, which allow him to travel back in time and save the world from the apocalypse. However, this comes at the cost of the very existence of the post apocalyptic time period, including the protagonists. Notable in that unlike literally the entire rest of the game, which is a tongue in cheek, over the top parody, the ending is played completely seriously.
The ending of The Orion Conspiracy is definitely this. Devlin found out who killed his son Danny, and the murderer is dead. The xenomorphs have been destroyed and the space station and asteroid have been blown to smithereens. Unfortunately, out of the 20 people making up the crew, Devlin, LaPaz, and Meyer are the only survivors. Their fates are left hanging. The matter of LaPaz being pregnant, and the matter of her unborn child being a human, xenomorph, or a hybrid is left hanging. There is a walkthrough that apparently aims for a Downer Ending.
Stolen has this for an ending. Breeze is (likely) dead, Richard Killian has been arrested for murdering his own goon Night. The previous mayor is back in power. Louie, Anya's partner, puts a Lampshade Hanging on the trope by saying that nobody is better off, but nobody is worse off either. Louie and Anya's apartment has been blown up, and so the two of them take off on a motorcycle, perhaps to go on vacation.
In The Witcher series, though the first game can end on a somewhat hopeful note, the second game ends this way no matter what you do. On one hand, Geralt is reunited with Triss, has recovered much of his memory, and knows Yennefer might still be alive. Unfortunately, the seeds of chaos have been sewn across the Northern kingdoms, and Nilfgaard is planning on marching in. Just about everything accomplished in both games has been rendered effectively moot.
L.A. Noire has Cole Phelps drowned in the sewers saving both Jack Kelso, his not-friend-but-not-enemy, and Elsa Litchmann, his love interest. The game ends with Jack attending Cole's funeral with Elsa and Cole's ex-partner Biggs. While the Suburban Redevelopment Fund is finished, the corruption endemic in the LAPD and Mayor's office, that chewed up and spat out Cole, is allowed to continue, and Roy Earle, Cole's crooked Vice partner and SRF bagman, gets to deliver Cole's eulogy. That Noir for you.
Prototype has Alex having destroyed the nuke to save New York City, but he is unhappy with the truth that he is the Blacklight Virus having been unleashed by the real Alex Mercer, his sister is in a comatose state, his ex-girlfriend has betrayed him, and the virus is yet to be stopped.
Dead Rising 2: Case West has good news, best news, bad news, and worst news. The good news is that Frank and Chuck escape with proof that Phenotrans is responsible for the Fortune City outbreak and evidence to clear the latter's name; the best news is that the evil company is going down. The bad news is Marian Mallon, the head of Phenotrans, refuses to release the permanent cure, as she sees only the strong ones will get it, and escapes with Isabela; the worst news is that nobody will believe what happened to Phenotrans.
Professor Layton games are fond of this. The best example is probably Last Specter, especially when you consider Arianna. Though they find the Golden Garden, which eventually cures Arianna of her sickness, they reach it at the cost of Loosha's life. Considering Tony and Loosha had been her only friends for nearly a year when everyone, including Arianna herself, thought she was a witch, it's more than a little heartbreaking to see Arianna begging Loosha not to go.
Unwound Future is also pretty bitter. Clive's giant robot is stopped from rampaging through London, but the Prime Minister gets away with the political backstabbing involved years ago from the first time travel experiment (yhough it is implied that Inspector Chelmey will try to take the case). Also, Claire's time in the present is up, and she must return to the past to her death. Then Luke has to move away, complete with a scene of him crying as he says goodbye to Layton, but Luke writes back often and seems to be fitting in at his new school well.
Baten Kaitos Origins ends this way. Verus and Wiseman are dead, Tarazed is destroyed, and Sagi and Milly elope, but Guillo is dead, Milly is orphaned, and the empire is in the hands of Geldoblame, who has apparently lost his mind. Also, if you've played Eternal Wings, you know Sagi and Milly die of a plague a few years later and their daughter is behind all the terrible things that happen in that game.
Corpse Party: Sachiko is convinced to let go of her rage and she and the other ghost children are finally able to find peace and move on, and the surviving characters are able to escape, but they are literally the only ones who will ever remember that the dead characters even existed.
Transformers: War for Cybertron: Optimus Prime and the Autobots have stopped Megatron's attempt to conquer Cybertron using Dark Energon. However, the planet's sentient core has been left partially corrupted by the Dark Energon and the only way for the corruption to be reversed is for the core to reboot itself, which will take thousands of years during which the planet will become unlivable, forcing Optimus to reluctantly order all surviving Autobots to evacuate Cybertron. Also, Megatron and the other major Decepticons (Starscream, Soundwave, etc.) are still alive and at large somewhere on Cybertron.
Batman: Arkham City: Though the day is saved and Batman's cured of the toxin in him, it wasn't without a cost - a portion of Arkham City is in ruins, almost 25% of the inmates are dead because of Dr. Hugo Strange's Protocol 10 along with Strange himself, Ra's al Guhl, his daughter Talia, possibly Clayface, and the Joker himself. Even more, Harley Quinn's pregnant with the Joker's child and she wants vengeance.
Norman Jayden from Heavy Rain has not a single unequivocally 'good' ending to call his own. Instead, most of his epilogues fluctuate between bittersweet and downright depressing. His two best endings fall under the former category. In 'Resignation', Jayden gives up on the Origami Killer case and resigns from the FBI. He states that he needs time to distance himself from the murders and get in touch with 'the real world' again. He also gives up the ARI, and it is implied that Jayden is putting effort into overcoming his addictions. In 'Case Closed', Jayden saves Shaun Mars and is hailed as a hero by the press, but his overuse of the ARI has caused him to start seeing vivid hallucinations. The epilogue has no spoken dialogue by Jayden, and ends with a shot of his surprised expression before fading to black. It is not revealed whether or not this condition is permanent.
In Star Wars Battlefront 2, you spend the entire campaign learning about an unnamed clone trooper who's been in just about every major battle, only to have the last mission be on Hoth, with him declaring that the empire has won, meaning he wasn't on Endor and knows nothing about the Empire's defeat, or he died on the second Death Star, making all the battles he's been in pointless.
It's even worse with the Kamino mission. He and the other stormtroopers stop the uprising, but have to kill their younger brothers in the process, and the Emperor replaces the old cloning template with the useless incompetent stormtroopers of the original trilogy, basically making the 501st the last of their kind.
Heavy Water Jogger: The good news is Mr. Fluke, owner of the biggest, most dangerous nuclear power plant in the USA and jogger, turned the heavy water back on, saved the plant, and got out of there alive. The bad news is the No Name Given disgruntled employee, who started the whole mess in the first place, has escaped, called the police, and pinned the crime on him. The police arrest Mr. Fluke. Then again, Alternative Character Interpretation seems to suggest that Mr. Fluke may have been a Bad Boss and Villain Protagonist, while the employee may be a Magnificent Bastard who wanted to take down Mr. Fluke.
Tenchu 2 ends with the Burning Dawn defeated, but Rikimaru & Ayame are the only Azuma ninja still around.
Warcraft 3 ended with the Burning Legion defeated for now, but Azeroth is still infested with undead and the World Tree was destroyed, forcing the Night Elves to come out of hiding. In the The Frozen Throne, peace is restored between the Horde and the Alliance, but Jaina had to kill her own father and Arthas succeeded in becoming the new Lich King.
Syphon Filter 2 ended with the Agency's conspiracy revealed and its leaders dead, but so is Teresa. Fans hated the last part so bad that it got retconned in the sequel.
Asura's Wrath ends with Asura destroying the source of all mantra, and eventually ending the world's suffering once and for all, but at the cost of his own life. As long as his daughter is safe, however, that's good enough for him.
Diablo III, for once, ends well. The prime evils have been vanquished forever, heaven is safe, and humanity is recovering the power it once had. But all of this comes with a hefty price: Many good people, like Deckard Cain and Leah, are killed, and Adria is still around.
Dragon's Dogma ends with the Arisen who became the Senechal and might continue to fight until another Arisen bests them. However, they stabbed themselves with the Godsbane sword, killing themselves. In the end, however, the cycle is broken, your pawn has a chance to live as a human being just like Serene by being you, and Gransys is recovering.
The true ending of Nine Hours, Nine Persons, Nine Doors is bittersweet as anything, what with the flashback scene with Junpei and Akane when they were children and the realisation that they can never actually be together, despite the fact that everyone (well, almost) got out relatively unscathed.
The optimist ending in I Miss the Sunrise. The universe is preserved at its current state — no more, no less. The war is over, but it has taken its toll — now there is even more work to do before society gets back to pre-Shine levels of stability. Neff, Chac, Cassidy, Cole, and Ivoronus are dead, and Tezkhra and Mahk have disappeared. Ros is possibly dead as well. As the ending title says, you pretty much have to believe that everything will turn out alright in the end.
The "Good" Ending of Avenging Spirit. The bad guys are defeated and your girlfriend is saved, but you're still dead with no way of coming back.
The ending of Grim Fandango. Manny defeats the Big Bad, gets the girl, and earns himself a ticket to the next world, thus finally reaching his initial goal of getting out of the Land of the Dead. However, he has to leave his best friend Glottis behind, because Glottis isn't a human soul but a native elemental spirit (though Glottis is happy with his new job and new friends that he was able to get thanks to Manny). Furthermore, it is unknown what exactly happens to a soul upon entering the Ninth Underworld, apart from the fact that none of the departed ever came back. The very last line in the game pretty much drives the point home:
Manny: "Nobody knows what's gonna happen at the end of the line, so we might as well enjoy the trip".
God of War ends this way. By the end of the trilogy, Kratos has all but destroyed the world during his campaign of vengeance. But he finally comes to terms with the fact that he was responsible for a lot of his own misery. He also finally forgives himself for his wife and child's murder, instead of running away from it. Kratos' final act is his most heroic one, as he sacrifices himself to bestow Hope — a power surpassing that of the gods themselves — upon humanity, ensuring that the world will recover. The survivors of humanity can rebuild civilization free of petty gods, titans, monsters, and even fate.
By the end of Policenauts, Jonathan leaves his friends and his daughter on Beyond to go back to his sad, lonely life on Earth. Many people that Jonathan and aforementioned friends cared about are dead. Beyond's future is uncertain with the exposure of Tokugawa.
The Walking Dead ends with almost all of its cast dead. Clementine survives, but she is alone after Lee is bitten and must be either abandoned or shot in the head. With Clementine's future uncertain, we can only hope that Lee's parting advice will help her.
Far Cry 3's good ending is this. On one hand, Jason and his friends safely leave the islands alive, and Vaas' Ruthless Modern Pirates and Holk's organized crime syndicate are both destroyed by the loss of their leaders. On the other hand, Citra dies to protect Jason from angry villagers, Jason is painfully aware of the fact that he now has to live with what he's become and the bodies of literally thousands on his conscience, Jason's brother Grant is still dead, and his friends are all left with mental scars from the brutal experiences. It's still better than the game's bad ending, which is pretty much exactly that.
Pier Solar And The Great Architects has one that might dip into Downer Ending territory a bit. Hoston, after killing Kloneo and Bethina, uses the complete Pier Solar to go back in time and undo some of the events of the game, such as the death of Mohu and Tagmor, and the death of Rudy, his father. In the process, he changes time so Hoston's mother ends up married to another man, ensuring that he will no longer exist, thus sacrificing himself, presumably so Alina and Edessot would not grieve over Hoston, as he changed time so he never existed in the first place. The music playing during this segment really pushes this toward a Downer Ending.
In RosenkreuzStilette, from Spiritia's point of view, her ending could be seen as part bittersweet, as she wonders what happened to Iris after she self-destructed her palace. Nevertheless, the rest of the ending is happy, seeing as how she feels good about her victory, and she happily reunites with everyone. Of course, as revealed in Freudenstachel, Iris is indeed still making mischief.
Grollschwert's ending is even more bittersweet. It ends with Grolla defeating Iris, but she self-destructs her palace and escapes, thus living to plot anew. Grolla escapes the palace, of course, and watches it collapse from a nearby cliff. She then goes to place a wreath of flowers at her grandfather's grave, and takes up his own Grollschwert for him.
The games have these whenever your character clears a one-player mode (whether it be Classic Mode, Adventure Mode, or All-Star Mode). After defeating every opponent and clearing every stage, and/or especially after defeating Master Hand, your character falls to the table, reverted back to his/her/its trophy form (in the original, its original form was a plush doll).
While the ending of The Subspace Emissary in Super Smash Bros. Brawl is happy for the most part, there's still a sad twist to it. Tabuu has been defeated by everyone and all the locations that were sent to Subspace are sent back to their rightful, respective locations, except for, strangely enough, the Isle of Ancients, and for a good reason; the detonation of multiple Subspace Bombs in the same location damaged the island so much that it was unable to return to the World of Trophies, and thus, a bright "X" is left where it originally was instead (which the playable characters triumphantly look onward at from a nearby ocean cliff). Since Tabuu is responsible for the destruction of the R.O.B.s through the use of the Subspace Bombs, this also makes the playable R.O.B., who disguised itself as the Ancient Minister throughout the story until near the end, the Last of His Kind.
Max Payne ends with Payne finally getting revenge against Nicole Horne and the Valkir business. After murdering the woman who offed his wife and infant daughter, and even shooting his way through the mafia and a skyscraper of mooks, Max finds that Woden meets his end of the bargain and gets him off the hook; however, this doesn't change the fact that Mona Sax is dead, that Max is still addicted to alcohol and painkillers, or the fact that he will never get his family or life back.
Max Payne 2 ends with Max finally coming full circle with his revenge, with him killing Bigger Badand "friend" Vladimir Lem and getting closure on his family's murder. To counter this, Mona Sax came back from the dead only to fall in love with Max and die permanently, Max was forced to kill Winterson, Vinnie Gognitti died horribly despite being a chump in over his head, and (as the next game shows) Max feels horrible guilt over the three dying because of his actions.
Max Payne 3 opens on Max no longer having anyone/thing to fight, but the ending lies on the happier end of the scale. Max has to murder his way through corruption and a freaking organ harvesting ring, all while watching the people he has to protect die due to his failings. On the lighter side, however, Passos comes through and saves Max (getting to leave and start a family), de Silva helps him bust the villains, justice is served, and Max finally comes to peace with his demons and addictions (earning himself a holiday in the process).
Phantasy Star IV: The Sealed Evil in a Can that has plagued Algo for over three thousand years has been defeated, and the souls of the heroes who lost their lives to protect the solar system can finally rest in peace... but the planet Parma is still gone, and the heroes who survived the battle have to return to their normal lives with no way to see each other again. Further, the environmental control systems, which have been slowly declining since their installation, have been damaged beyond repair; although Wren and Demi have stabilized them and will watch over them for as long as possible, there will eventually come a day when the system finally dies, and the remaining planets will return to their natural climates: a freezing wasteland, and an arid desert, respectively, neither of which were ever meant to support Parmanian life.
Jack French: The ending for the third game. Jack may have killed Vince, the Big Bad of the entire series, but he got killed as well.
In The Last of Us, Joel saves Ellie from being killed by the Fireflies and the two are free to live out their lives in peace. This comes at the cost of a possible cure for the cordyceps and Joel having to lie to Ellie about the circumstances behind their escape.
In the Wii version of A Boy and His Blob, after defeating the evil emperor for a second time, the blob has to return to his planet while the boy stays on Earth. While this is pretty much expected, the credits bring it to Tear Jerker levels as they are accompanied by a pretty heart-wrenching song called "Everything to me", which is about how much the time they spent together meant to the boy, coupled with some drawings of both characters playing together.
They don't get much more bittersweet than the ending of Brothers: A Tale of Two Sons. Although the boys reach the mystical tree that contains the water which will cure their father's illness, the older brother dies and the younger brother must press on without him.
Both of Danganronpa's endings are pretty bittersweet: in the 'bad' ending where Naegi calls out Kirigiri on her mistake, Kirigiri is killed and the rest of the survivors cave in, staying inside the school forever (and starting up a family, which kinda makes it a little less bitter). In the 'good' ending where Naegi stays silent, he ends up being saved by Alter Ego and Kirigiri, making Junko Enoshima submit to her own 'punishment', and escaping the school with the remaining crew. Unfortunately, what makes this a bittersweet ending is that the world outside could be post apocalyptic, and Junko never actually confirmed nor denied it before her death...
The "good" ending in The Halloween Hack. Dr. Andonuts dies, but the monsters have been stopped, and Varik is returned to Twoson.
Risk Of Rain's ending is, for almost all the characters, like this. The creature that shot down your ship is dead, and you've carved a swath of carnage and death across the whole planet, have exposed yourself to so many dangerous agents and artifacts so as to mutate and change into something not particularly human, and are finally able to reach the ship's controls. And so you left, your mind utterly shattered, and your humanity lost to the very things that let you keep your life.
The Last Story ends with the war between humans and Gurak terminated, ending with both races living together in peace. Also, the Outsider is reassembled and it flies to space where it belongs. Calista marries Zael, and even gives him the title of Knight he has been dreaming of. However, the characters lament that Dagran had to be killed when he revealed himself to be a comrade of Zangurak, though he manages to redeem right before his death. It'a also revealed that, despite his questionable ambitions, Count Arganan was not purely evil like he thought, and even the otherwise jerk-acting Jirall had earned an undeserved death after he slipped into insanity as a result of Dagran having falsely accused him for the death of General Asthar, which was actually Dagran's crime.
In The House Of The Dead Overkill, G and Issac stop Papa Cesar and Clement from unleashing their plans, but Varla's brain ends up getting separated from their body, and the last boss fight was against the mutated form of it.
Gears Of War 3 ended with a superweapon created by Marcus' dad going off, causing every single non-human threat, Locust and Lambent alike, on the planet to be killed (actually, more like vaporized), and left very little room for doubt about whether any of them had survived. But aside from the vast majority of humanity being killed in the previous years, Dom and Marcus' father dying (just after re-uniting with him, believing him to be dead for a long time) just before the end of the war, and the small remnant of humanity's resources already being extremely limited, nearly the entirety of the surface of the planet along with most of its natural resources were decimated during the war (by the Hammer strikes in particular), making any chance of ever rebuilding extremely slim. Life's going to be tough for humanity from here on out, any way you slice it.