In many a video game with Multiple Endings (and, in the majority of RPG cases, a Karma Meter), the "good" ending will be the canonical one. Rarely will the "bad" ending be canonical, or the "bad" side actually canonically win. This may be because there is less appeal in a Downer Ending, or simply because having the villains win wouldn't be financially conducive (because it would probably end the series right then and there). It may be necessary for the sake of having the protagonists of the first entry be recurring characters.
In any case, much as the "bad" side rarely gets its own campaign, it often doesn't get its canonical ending.
Take note; when this trope is subverted, it can serve a discrete narrative purpose: If Evil wins, Good can come back next time and vanquish the enemy even from a position of weakness. From a player's perspective, it makes previous (righteous) efforts less meaningful, but makes winning his current battle more rewarding.
Sometimes a subtrope of Cutting Off The Branches.
The "evil" ending for Might and Magic VII was originally intended to be canonical by the game developers, but they ended up going with the "good" one, instead.
The reason for the change was that the evil ending was planned to lead up to Armageddon's Blade, but a very negative reaction from part of the fanbase to some of things planned (a new cybernetic faction based on the technology gained by the evil side) led to that having to be scrapped in favour of a more standard fantasy story.
In Heroes of Might and Magic II, you get to choose whether to play the good or evil campaign (and then later on whether or not to redecide). The sequel Heroes of Might and Magic III, however, counts the good side as canon.
Heroes I tells us the Warlocks and Barbarians are Evil, and the Knights and Sorceresses are Good. The canonical victor is the Knight Lord Ironfist. Of course, the actual story is a bit barebones, and the only major chunk is in the manual... which doesn't exactly present Lord Ironfist as an unambigiously Good Guy.
Both Knights of the Old Republic games canonically have light side endings. Thus far this only matters for the Star Wars canon outside of the games, though — and even then this is mostly theoretical for the sake of official timelines and such (all actual narrative media, like the KotOR comics, have left the events of the games ambiguous). In the games themselves, KotOR II allows you to decide whether the Light or Dark ending happened in KotOR I, and it seems like The Old Republic, by taking place centuries after KotOR II, will permit a similar level of ambiguity about both games. It seems that no matter what you do, the galaxy keeps reverting to a basic Crapsack World state.
Interestingly enough the Dark Side KOTOR ending came pretty close to overwriting the canon LS ending and averting this with a deleted scene produced for Star Wars: The Clone Wars, where Filoni wanted Revan to appear with Darth Bane as advisers of The Son in the Mortis trilogy, but the idea was shot down by Lucas, through models for the Sith Lords were made. Had Filoni suceeded in implementing this idea it could have over-turned the canon LS ending in KOTOR and created an aversion of the Light Side canon rule.
In The Old Republic, the events of Knights of the Old Republic don't usually come up very often (since those games took place three centuries before the MMO), but when they do, the first game's Player Character and the Exile were Light side. (The first game's Player Character, for example, helped the outcasts on Taris get to the Promised Land). For the MMO itself? The Enyclopedia zig-zags it by implying the Light Side options are canon for the Republic players and the Dark Side actions canon for the Sith faction (as evidenced by the Sith Inquisitor's final title Darth Nox, which you only get playing as a Dark Side character).
The original Jedi Knight game had two endings: In the Dark Side one, Kyle becomes the new Galactic Emperor. Naturally, the canonical ending is the Light Side one, where he relinquishes his powers.
It's also interesting how if you pick the Light Side, you get cut scenes and a plot that ties itself up nicely. If you pick the Dark however, you barely get some exposition text that (barely) justifies doing the exact same missions and actions, but for yourself apparently.
The sequel, Jedi Outcast, only has one ending. The spin-off, Jedi Academy, has both a Light and Dark ending; Word of God is that the Light ending is canonical, which is where the novel starring Jaden Korr follows from.
The Command & Conquer series started out playing this straight, however with Firestorm onwards, this trope is averted in the main continuity. The Red Alert timeline plays it straight throughout, though.
The canonical ending for Shin Megami Tensei I, as it would appear from Shin Megami Tensei II, is not the Law or Chaos endings (each of which have their bad points, one more than the other), but the Neutral ending. As the Neutral ending is the only one that acknowledges that both sides, in the end, are jerkasses, it's as close to a "Good" ending as one can get.
Disgaea always uses the Good Endings, since the Bad Endings tends to be... really, really bad. Also, the Good Ending ensures that all the important characters are alive and well so they can make cameo appearances in the following games.
Interestingly, while almost all Disgaea games work from the good endings, both Prinny PSP games work from the bad ending of Disgaea.
The endings of Tales of Symphonia vary only slightly, but the ending in which you kill Zelos, resident Casanova and Double Reverse Quadruple Agent, is considered non-canon: he appears in the sequel, and the endings to the manga and the anime both keep him alive.
Metal Gear Solid had two endings, both of which were congruent with Snake's character. Metal Gear Solid 2 avoided talking about which ending was canon as much as possible; it wrote out the character whose life depended on the Good Ending except for a bitter joke Snake makes about her. The on-disk supplemental material even implied both endings — "The Shocking Conspiracy Behind Shadow Moses" says the Intrepid Reporter finds a bandana on the beach (which Meryl picked up and gave to Snake in the Good Ending, suggesting she didn't survive to find it), and "In The Darkness Behind Shadow Moses" omits the scene where Meryl's fate is decided, but has the narrator say that it seemed like he had managed to save Meryl at the end. Then came Metal Gear Solid 4, showing her alive.
To make it even more ambiguous, the first thing we see Snake do is jump onto a ship using invisibility Camo, which is what you get from the ending where Meryl dies. But then near the end of the game, when Raiden asks Snake about his ammo, Snake points to his headband, which Snake gets in the ending where Meryl survives.
The Resident Evil series takes it to a particularly far extent. In the first game, none of the endings are actually canon, as the official version of events is impossible to achieve in an actual play-through — most notably, there's no way to get everyone out of the mansion alive in RE1 (You'll never even meet at least one character), yet canon dictates they all survived.
Total Annihilation canonized the Arm campaign version (and therefore good-guy victory) when the expansion pack "The Core Contingency" was about the victorious Arm having to deal with a backup Core Commander seeking to destroy the galaxy.
In Overlord II, it is made clear the canon ending for the original game could not have been the 100% corruption one. However, the 0% corruption"good" ending is not enforced either. As only two corrupt actions in the original contradict the sequel, the canon Overlord could be anywhere between 0-80% corrupt.
Just about any fighting game character ever who qualified as a villain. It's so blatant, in fact, that the moment you see it, you know right away that it's not going to stick. M.Bison takes over the world ("of COURSE!")...uh, no. Fulgore spearheads Ultratech's enslavement of humanity...come on. Heihachi kills both Kazuya and Jin...he wishes. The Orochi cultists finally succeed in reviving him...not. Raiden's buddies didn't blow up the planet, either.
Dawn of War: Winter Assult features four possible endings: Imperial Guard, Eldar, Chaos, and Orks. While the eldar campaign was originally thought to be canon, (as both Farseer Taldeer and Gorgutz live on to Dark Crusade), an artifact in the Retribution campaign revealed that Sturnn managed to secure the titan, which contradicts the ending of the eldar campaign where it is blown up. So the most likely ending is that the Imperial Guard was the canon winners and Taldeer managed to escape.
Further muddling the issue, a Only War sourcebook reveals Sturnn was killed by the Eldar on that planet and makes the Eldar campaign canon (although Sturnn is implied to survive in the game's eldar ending).
The Dark Crusade and Soulstorm campaigns possess seven and nine potential endings respectively. Dawn of War II states that the Blood Ravens won the former: The only thing known about the latter is that the Blood Ravens lost, and badly. Though considering how notorious anything in Warhammer 40,000 is with unreliable narrators, neither of these statements are exactly reliable.
In the sequel, Retribution makes one of the two 'purest' endings from Chaos Rising the canon one: Diomedes is alive and joined Gabriel's rebellion, Avitus is revealed as the traitor, and Cyrus and Martellus are playable squadmates during the Space Marine campaign, while Davian Thule and Jonah Orion make cameos, Tarkus is revealed to be The Ancient, and the Force Commander's Thunder Hammer is one of the ultimate weapons. The evil endings for Chaos Rising includes the entire party being sent on penitent crusades, the execution of the Force Commander (the player) and his name being struck from the Chapter in disgrace, and the whole group betraying their chapter and joining the Black Legion. None of the three would allow for the above to happen.
In King's Quest VI, the storyline branches into two towards the end, each with a very different way to finish the game. In addition, there are a number of triggers that affect the final cutscene. Your actions affect whether there is a wedding ring, whether both families attend the wedding, who is alive or dead, and so forth. The novelization treats the longest "good" path as the real one.
Fear Effect 2 has two endings based on a choice near the end. The main character can shoot her girlfriend Rain, leading to a bad ending. The game is a prequel to Fear Effect, where Rain doesn't appear. Bury Your Gays? Nope, the good ending is the canonical ending, and Rain just doesn't happen to be on screen in Fear Effect.
Fear Effect itself has 3 possible endings, with every character dying at least once in two of them. On hard, however, all 3 survive.
At the end of Ultima VII (part 1), you are given the choice of destroying the Black Gate, or going through it and allowing the Guardian to enter Britannia. The future games all assume you destroyed it. Some fans have noted, though, that Ultima: Ascension (note the lack of number in its title) works better as a sequel to the Evil Ending of Ultima VII than as a sequel to Ultima VIII.
The second and third installments of X-rated Visual Novel series Inyouchuu assume the player got the best possible endings in the first and second games, which makes sense, considering the bad endings generally involve the main characters being killed or enslaved.
Done with little subtlety in The Neverhood, where you can make a choice between Good and Evil at the very end of the game. The fact that the Good ending is the true one is already very obvious just through the sheer length difference between the two final cutscenes, but the Actionized SequelSkullmonkeys explicitly starts from the Good ending, though not without a twist: the Big Bad, whom you'd presume to be dead, survives and continues his evildoings on another planet, requiring you to get rid of him again.
Streets of Rage has a bad ending should one player accept Mr. X's offer and the other refusing. This results in both players fighting to the death, then the survivor fighting Mr. X to overthrow him and become the new evil overlord of the crime syndicate. However, the sequel assumes that the main characters chose wisely and fought Mr. X right away instead of fighting him for his power, since Mr. X comes back in the sequel.
The endings to Fallout 1 and Fallout 2 assume all of the 'good' choices were made, even options that are only theoretically available due to bugs disallowing the player from achieving the perfect endings without mods. Though Fallout 1''s good Brotherhood ending isn't canon — as shown in later games, the Brotherhood ends up somewhere in-between the good and evil endings.
The ending to Fallout 3 is also thought to be the good-karma choices, and one of them is confirmed in Fallout: New Vegas: When Megaton's shopkeeper/eccentric scientist Moira Brown asks you to do research for a "Wasteland Survival Guide", you give her useful information, vague half-truths, or ridiculous lies. The book appears in New Vegas and has helped a lot of people.
Neverwinter Nights 2: Mask of the Betrayer presumes the player defeated the King of Shadows instead of siding with him.
Granted, it's a heck of a lot easier to write it as the Founder rescued you from the King's collapsing lair than try to figure out how to get you out of the King's clutches the other way.
Apparently averted by way of Fridge Horror in Storm of Zehir. The second expansion takes place after MotB, and the Token Evil Teammate One of Many appears in a random encounter. Obtaining One of Many requires a consciously evil act on the part of the Knight-Captain.
Not neccessarily. If you exorcise the weaker spirits in the furnace (eternal Rest or Devour Spirit) rather than free the spirits within (provoke spirits) The Many states that eventually it will reform so that could be what happened.
In inFAMOUS, Cole is canonically a hero, though Infamous 2 allows you to play starting from a karma based on your previous runthrough, starting you halfways into the karmic rank you inherited and changing the dialogue in later dead drops. inFAMOUS: Second Son , on the other hand, clearly follows from the hero ending of Infamous2. It's worth noting that this is precisely because an immense majority of players of Infamous2 were noted from trophy data as favoring the hero ending.
In Winter Shard, Frederone can be a total bastard who kills and mistreats everyone in his path and even dethrones the Evil Overlord himself, but the true ending requires him to be as considerate and thoughtful as possible to those around him and ultimately go the redemption route.
Shadow the Hedgehog has nine different endings, and each of them are bad or good in their own way. However, even if you make Shadow be purely evil, the Last Story segment is considered canon, where Shadow sides with the forces of good.
Games from the Geneforge series have a wide spectrum of endings, from overwhelming victory of Shapers to overwhelming victory of rebels. It is hard to say which side is more wicked, especially toward the end. The sequels choose an intermediate ending (usually the rebels' narrow victory), which also tends to be the least bloody, playing the trope mostly straight. However, the "nicest" ending for the first game is probably the victory of Trajkov/Trakov, making the second game an aversion.
The first Gabriel Knight game has three possible endings; Gabriel dies in both the "neutral" and "bad" endings. Considering that there are two sequels and plans for a third, it's pretty clear which ending is canon.
The second game in the series includes a Non-Standard Game Over if you screw up a task at a specific point near the finale, revealing that Gabriel dies, and Grace is arrested on suspicion of murder. Once again, this clearly bears no relation to series canon.
Metro 2033 had two endings; a good one, and a bad one. The sequel, Metro Last Light, averts the trope by continuing on the bad ending where Artyom chose to nuke the dark ones. Kind of a Broken Aesop, since the bad ending in Metro 2033 basically told you how much of a douche you were, since the entire game was determined to avoid that ending. It doesn't help that it's the same way the book the game is based on ended.
In Soul Calibur, endings tend to be an amalgamation of several character's endings. And not always the good characters. Siegfried's ending in Soul Blade where he becomes the new wielder of the Soul Edge is canon (Though he didn't fight Cervantes directly, only Soul Edge itself.)
Colony Wars, where the second-best ending in which the League of Free Worlds withdraws from Sol and closes the jumpgate as they leave, sealing off the remnants of The Empire from the rest of the galaxy, as opposed to triumphing over the Empire outright is used as the background of the sequel, Colony Wars: Vengeance, which involves not only a Perspective Flip where you're on the side of a long-since post-apocalyptic Empire which has been pulled back together by a charismatic leader to strike back against the League, but also drops several clues to the effect that said charismatic leader is the player character from the first game gone absolutely insane.
Blizzard averts this in Starcraft and Warcraft III by making all the campaigns sequential parts of a larger narrative. Notably, in both cases, the good guys win in the game, but the bad guys in the expansion.
Averted in Warcraft I, as the Orc ending, in which daemonically corrupted Orcs overrun the continent, is canon though some aspects of the Human campaign (like killing Medivh) are also integrated. The sequel also does this with the roles reversed, so the humans win, but some aspects of the Orc campaign are also canon.
It was never made completely clear which campaign of the Beyond the Dark Portal expansion was canonical until World of Warcraft's "The Burning Crusade" allowed players to enter Outland and meet the Alliance heroes there (thus confirming that the Alliance campaign was the one that happened).
Some elements of the Orc Campaign are included: Teron Gorefiend's raids, the Warsong, and a fraction of the Shattered Hand clans left behind on Azeroth and Ner'zhul's escape.* Some of the Alliance campaign is, through retcons, not included. In fact, the Alliance campaign ends with the narrative that Kadghar led their remains through one of the new portals in the hope of finding their homeworld again, yet none of this seems to have happened in the Burning Crusade. All in all, a mixture of the two seems to have happened.
Total Annihilation: Kingdoms, like Starcraft, has every mission as canonical...though rather than discrete campaigns, it is organized in the rather odd way of the player taking over random countries in turn, and even at some points e.g. fighting to gain a beachhead before then taking command of the other side to try and destroy that beachhead.
The True Endings of the first two BlazBlue games are largely neutral, with both happy and downer elements and neither side getting a clear victory.
Shadow Hearts 2 went off from the bad ending of Shadow Hearts, while Shadow Hearts 3 most likely went off of the good ending to ''SH2'', though this is up for debate.
Since the good ending to SH2 seems to imply that Yuri will be stuck in a loop until he manages to save Alice, both games effectively have the good ending as canon (simply so SH3 can happen).
In Silent Hill 4, however, Henry will remark that his landlord, Frank Sunderland, claims his son (i.e. James, the protagonist from the second game) never returned from Silent Hill, but it's never made clear whether that means James canonically suffered a Bad Ending or just lost contact after leaving Silent Hill with Laura in the Good Ending, mirroring Harry going into hiding with baby Cheryl and giving them new identities in the Good Ending of the first game.
The "Bad" (more like evil) ending is canon for Legacy of Kain: Blood Omen. Though that might have been a Double Subversion. Turns out it was better in the long term for Kain to not sacrifice himself.
Half-Life 2 runs with the idea that you have chosen to join forces with G-Man instead of going for the Doomed Moral Victor scenario. This makes sense, as the first is the one that lets the player character be alive for the sequel, but neither can really be said to be a "good" ending, as it is the result of The Sadistic Choice. Some fans have argued that either works, since we never actually experience Freeman's death and the G-man could just be messing with him to prove a point. This would be consistent with the gameplay and story theme that 'The One Free Man' doesn't really have any choices, and goes wherever he's railroaded.
In a more amusing aversion, near the end of Episode Two, it's shown that Gordon ruining someone's lunch in the first game by leaving it in the microwave too long is canon (it was Magnusson's).
Castlevania: Dawn of Sorrow features an alternate play mode that occurs immediately after the game's Bad+ ending, wherein Soma becomes Dracula and it's up to Julius, Yoko, and Alucard to stop him. It's difficult to say whether this will stick, though, as Dawn of Sorrow is currently the last game in the series, chronologically.
Somewhat disturbingly, The 11th Hour operates on the premise that the player lost The 7th Guest (this is not made clear at the outset, but becomes obvious as you go on). Trilobyte claims that had they gone on to do a third game, it would've been an alternate sequel to The 7th Guest rather than a sequel to The 11th Hour where the player won the final battle against Stauf — and thus been less of an unrelentingly dark game and also, possibly, given us some actual character development of the eponymous character in The 7th Guest (who would have again been the protagonist of the third game).
Note that none of this has much to do with the much later proposed (and failed) attempt at making a sequel, The Collector, which seemingly has nothing in common with the first two games except the character of Stauf along with some general thematic similarities.
Star Control: The first game features an interstellar war between the Alliance of Free Stars and the conquering Ur-Quan Hierarchy. At the beginning of the sequel, you learn the Alliance lost handily, and humanity and the rest of the Alliance races have been enslaved by the Ur-Quan.
... mind, the Hierarchy won using a ship they didn't have in the first game...
Averted in The Elder Scrolls II: Daggerfall. At least half of the sides are jerks, or power-hungry, or have ill-reputed connections. The most "Good" ending is probably to give it to the Underking. According to Word of God, because of the activation of the giant brass golem Numidium causing the god of time himself to screw-up, ALL of the endings occur simultaneously and all the contradictions cancel each other out.
The Elder Scrolls is kind of an interesting example in general - the sequels each assume that the storylines of the previous games were completed (though not necessarily by the same person), but anything optional is left ambiguous (for example, in Tribunal, [Almalexia kills Sotha Sil, and then the hero kills Almalexia, leaving Vivec the sole remaining member of the Tribunal, but very much an option for further deicide — Azura specifically tells the hero to kill him after finishing with Almalexia. Meanwhile, in Oblivion, in the Pocket Guide to the Empire that comes with the Special Edition, in reference to the previous game it says that the "supposed" Nerevarine has left to check out Akavir of all places, while Vivec has disappeared from his temple, making it impossible to be sure whether or not the hero killed him in Morrowind — but Almalexia and Sotha Sil are canonically dead.
In the case of Skyrim, however, it's heavily implied that the Champion of Cyrodil participated in the events of the Thieves' Guild and Dark Brotherhood before eventually becoming Sheogorath through the Shivering Isles DLC.
Midway through UFO: Aftermath, the invading aliens have a proposition for you, cease hostilities and have them create a space station for you and the rest of the human survivors, so they can finish changing Earth into a living psychic supercomputer slash weapon, with humanity having a say in controlling it. Accepting is a Non-Standard Game Over, refusal leads to you wiping said aliens out. The sequel, UFO: Aftershock, however, assumes you accepted.
Star Wars: Empire at War, Imperial story. The missions leading up to the ending are canon, but the ending itself (the destruction of the Rebellion with the Death Star) isn't, obviously.
Sonic Adventure 2 uses selective editing to make both sides' endings true: the dark side ends with Eggman seeming to have accomplished his goal, but zooms in to a warning message that he ignores, which, in the hero story, is shown to be because Sonic sabotaged his plans at the last minute. Of course, both plans lead into the last story where Eggman fails to take over the world, so in the end this trope is in fact used.
The reason why both the Hero and Dark endings are canon is because there is The Man Behind the Man who wishes to destroy the world whereas Eggman simply wants to take it over. Both sides cooperate to stop his plans. In other words, the Dark characters accomplish their goals, but those goals changed drastically from when the story began.
Sort of done, in Avernum III. While it's canonical that Erika dies in her duel with Rentar-Ihrno, there is a much harder way to win the game, that preserves her life. You just have to never accept the plot token she gives you, leading to much harder battles in the end game, and having to fight the final battle several times.
Mass Effect mostly avoids the trope by avoiding establishing any of the player-choice elements as canon. However, starting Mass Effect 2 without importing a save from the first game leaves you with a default backstory matching the first game's Renegade ending, rather than its Paragon one. (The interquel novel Ascension basically hand waves the end of the first game in a sort of nihilist fashion.)
The canon ending of Clock Tower: The First Fear, is either A, B, or C, since D-H show Jennifer dying and S shows one of Jennifer's friends surviving.
Fatal Frame: the canon ending for the first game is that Mafuyu stays behind with Kirie; even though you survive, it is still not exactly a happy ending. In 2, the canon ending is that Mio had to strangle Mayu to complete the Crimson Butterfly ritual; again, although everybody is now free from the eternal torment, still a Bittersweet Ending. In the much happier ending added in the Xbox exclusive version, both sisters survive and Sae is reunited with Yae in death. In 3, the two endings decide between whether Kei survives or not, while as Mio survives in the Good Ending, but her fate is not mentioned in the first. However, neither of the endings have been officially declared canonical.
Command & Conquer: Generals features an episodic campaign that showcases the viewpoints of all three sides and runs in chronological order. This continues in the Zero Hour expansion.
As mentioned above, the titles in the Tiberium timeline starting with Firestorm onwards avoid this trope by having both campaigns occur simultaneously. This includes the hidden Scrin campaign in Tiberium Wars, though that campaign starts around the midpoint of the GDI and Nod campaigns.
BioShock 2 avoids the issue as well by having the sequel take place ten years later, with a very different main character, and no definite answer to the original's ending. The multiple endings are nodded to in the second game, as you find a group of splicers arguing over what Jack did at the end of his journey; neither of them reach a conclusion that they can agree on.
Bioshock Infinite demonstrates the existence of multiple universes, so technically every ending is canon in some reality. However, the Burial at Sea DLC establishes that the good ending of BioShock is canon.
One wonders whether this trope is averted (and what constitutes "canon") in old-school arcade games like Space Invaders where the game continues forever until the player is defeated (and hence by implication the only possible outcome is one where the aliens win?) Space Invaders in particular dodges this issue by having the various "sequels" and spin-offs not actually take place in the same "continuity" as the original — in one of the sillier ones, the original is a Video Game in-story that inspired the aliens.
Blaze Union's most depressing ending (in which Siskier dies and then Gulcasa's friends Jenon and Medoute betray him) is canon. Due to some obfuscating translation choices by Atlus, Yggdra Union's D ending is often mistaken to be canon, although that's not the case — in all Dept Heaven games except Riviera, the A ending is the one that's canon regardless of how "good" or "bad" it is.
The sequel to The Suffering defaults to beginning from the first game's neutral ending, although the good and evil endings also lead into the plot. Importing an old save allows you to start from the good or evil ending, and beating the game allows you to choose which to start from on future playthroughs. (Which ending you begin from does have an effect on what happens in the rest of the game.)
MechWarrior 4: Black Knight assumes that Ian Dresari let his sister die in the original game and has since become a tyrannical despot.
Deus Ex: Human Revolution doesn't have any explicitly good or bad endings, but with what the player learns, the Illuminati seek to prevent augmentation because it threatens their control, so Sarif's ending could arguably considered more good in principle. However, it being a prequel to Deus Exheavily implies that this did not happen, but one of the other endings did.
Not a video game example, but a recent Magic: The Gathering block, Scars of Mirrodin, revisits the previously-detailed plane of Mirrodin, now the site of a battle between its natives, the heroic Mirrans, and the Phyrexians, the fan-favourite villains from the Weatherlight saga (and quitepossiblythe worstpeopleinexistence). For the final set, Wizards of the Coast previously released two logos, set symbols, and titles for each side, to prevent spoiling who would win — the Mirrans would have Mirrodin Pure, and the Phyrexians New Phyrexia, with one set being fake and the other to become canon. As it turns out, thePhyrexianswin.
More "batshit" than "wicked", but NieR results from the bonus fifth ending of Drakengard, rather than the good ending that leads into Drakengard 2.
The Mega Man X series may be the ultimate aversion: Every subsequent game has assumed the worst possible ending from the prior game if it had multiple endings, up until Mega Man X6 where Zero did not seal himself away after all. This was done mainly so people could still play as Zero.
And even on X6, the bad ending was supposed to be canon, it was just retconned so the series could continue.
Splinter Cell: Conviction assumes that the player killed Lambert in the previous game, Splinter Cell: Double Agent.
Corpse Party: Blood Covered plays with this in its sequel, Book of Shadows. The game is divided into several chapters, most of which follow Blood Covered's final Wrong Ending, where Satoshi suffers a "Groundhog Day" Loop back to when they performed the ritual and is forced to return to Heavenly Host. Things play out differently this second time through, as some of the other survivors gradually recover their memories. This is treated as an Alternate Timeline. Other chapters are set during the events of Blood Covered, giving certain characters A Day in the Limelight — and, in one instance, A Death in the Limelight, revealing the events that lead up to her death in one of the longer Wrong Ending paths. Only the game's final, unlockable chapter follows the prior game's true ending, with a major Sequel Hook.
The "bad" ending to the original Blood Omen: Legacy of Kain is the one from which all the remaining Legacy of Kain games derive. Kain destroys, rather than restores, the balance of the Pillars by refusing to sacrifice himself, thereby creating the much darker, emptier and more harrowing version of Nosgoth that is the setting for the rest of the series.
Vampire: The Masquerade – Bloodlines has five possible endings. The novel Gehenna: The Final Night loosely follows on from the events of the game, but the only ending to be explicitly ruled out is the Strauss/Camarilla ending, and the PC's fate is never revealed.