In Dragon Quest I, when the player finally faces the Dragonlord, he offers the choice to join him and rule half the world. If "no" is selected, then the player engages in battle and gets a good ending after defeating him, but if the player chooses "yes", the player gets a bad ending. Defeat the Dragonlord and you get one of the three good endings based on where the princess is when you return to the castle (you brought her to the castle before killing the Dragonlord, you arrive carrying her after killing the Dragonlord, she's still imprisoned in the cave). The (minimalist) end game cut scene varies a bit for each ending. In the last one, the hero travels off to faroff lands alone.
In Dragon Quest V, the ending can be altered depending on the player's choice on who the protagonist should marry halfway through the game.
Phantasy Star III, which alters depending on the marriage choices made by the player through the game.
The endings of Fallout and Fallout 2 are a series of short epilogues detailing the future of the different settlements the player visited, with multiple endings highlighting the player's actions and their moral implications. For example, in Junktown of the original Fallout, the player can make the good choice of siding with the sheriff against the greedy casino-owner. If the player sides with the Sheriff, the town becomes a bastion of law and order. If he sides with the casino owner, it becomes a Wretched Hive.
Oddly enough, the Fallout 2 manual's autobiography by the Vault-Dweller seems to indicate the original idea for Junktown is canonical.
Fallout 3 and Fallout: New Vegas also have the "segmented ending" type, with different pictures depending on the player's karma and deeds; for example, if you have Evil karma and nuked Megaton, a montage of its destruction is shown. Each has their own music piece as well.
In the former, the epilogue DLC Broken Steel is also affected by the player's ending choices: if you sent Lyons into the control room, she will be dead (as opposed to comatose if you or a radiation-proof follower activated it), and if you infected the purifier with the Modified FEV, consuming Aqua Pura will be fatal to the player and the clinics will have many dying patients.
New Vegas in particular has four very specific paths that factor heavily into the epilogues depending on which faction you support. Specifically, there's the NCR, Caesar's Legion, Mr. House and the Wild Card path.
In the Pokčstar Studios in Pokémon Black 2 and White 2, you can shoot several movies. Depending on whether you follow the script, do the opposite, or Take a Third Option and do something entirely different, the movie will either have the "Good", "Bad", and "Surprise" ending. Getting the latter results in more rewards and a higher score.
In addition to the "slideshow" mentioned above, Arcanum: Of Steamworks & Magick Obscura has a more traditional approach to multiple endings: when you get to the Big Bad, you're given the option of either destroying him (your original goal) or siding with him. The latter leads to a bad ending where your character rules over a world now completely devoid of life.
Which is somewhat dissonant with the buildup to that choice. If the player sides with Kerghan then it is with full awareness that he plans to kill every living thing, the player and himself included. Yet the game portrays it as some shocking Face-Heel Turn when it says that Kerghan eventually "turned" on the player.
Nippon Ichi games such as the Disgaea series and Makai Kingdom, which also include a number of Nonstandard Game Over endings as well. One of their earlier games, La Pucelle: Tactics, gave most chapters within the story multiple endings, but only one final end. Well, unless you complete all the optional dungeons, which grants Prier a unique change of character... (And may be canon, considering her cameo in Disgaea.)
It should be noted, that aside from the first game, you actually have to put effort in to get a normal or bad end, such as killing over 100 team members in combat, while the true end is given by default. In the first game, killing ANY team member, even by accident locks you out of the true ending. The game does not tell you this, as the series evolved the other endings rely less on team kills to the point the fourth game doesn't bother to track them. (The alternate endings are instead defined by play-set relationships to the protagonist, defeating bonus bosses, or being at a set level.)
Most of the Atelier games (published in the West by Nippon Ichi) have multiple endings; some of the earlier, free-form Atelier games have upwards of thirteen of them, ranging from good to bad. The Iris sub-series mostly did away with this, but for the Mana Khemia games and the Atelier outings on the DS, the concept returned with vengeance. It'll be back IN THE THUNDERDOME! with the upcoming Atelier Rorona for the PS3; that game is being touted as having thirty such endings of various types, among the highest count in the history of the medium.
It actually doesn't. There's 4 "quality" endings, dependent on how well you do with the store and how well you get along with the town populace, one for each secondary party member totalling 6, one for essentially getting everyone's character ending in one playthrough, one for being rich, one for making pies, and one for being an adventurer. That's a total of fourteen. However, only one of them can be gotten in each playthrough. It's quite a lot of work for Trophy hounds. The rest are essentially Game Overs.
Chrono Trigger and its sequel, Chrono Cross, had dozens of different endings depending on when you fought the final boss (who can theoretically be fought at almost any point in the game, but only in a New Game+ would you be expected to actually be able to do it):
While a cat in the Developer's Room tells you Chrono Trigger has 10 endings, it officially has 12 endings, 2 more if you count Non Standard Game Overs, and one more for the DS Updated Re-release, giving us grand total of 15. Moreover, the 2 "normal" endings that are easily achievable without a New Game+ have two major variations each depending on whether or not you crash your time machine, and several smaller ones, for example managing to save Lara. Two of the other endings are basically just glorified credit rolls, though.
In Chrono Cross, you could only fight the last boss at any point in New Game+, due to only actually having the item necessary to do so there. Here, what characters you had in the party at the time also changed the ending as well.
Given that you have forty-five characters, you have to beat the game no less than 23 times just to see all of the possible character responses.
When MOTHER was translated, there were some changes to the game, even to the sprites themselves. The ending is included in the changes. When Giegue flees in the original Japanese version, Ninten, Ana, and Loid turn around and stand there as the credits roll steadily behind them. Once "To Be Continued..." shows up, pressing a button makes the trio disappear. In the Updated Re-releaseMOTHER 1+2, when Giegue flees, an epilogue plays, showing: Ana reunited with her mother, who was abducted by Giegue; Teddy revealed to be okay and belting it out at the Live House; the kids in Youngtown reunited with their parents, who were also abducted; Ana returned to her house and telling Ninten and Loid that she'll never forget them; Loid being congratulated by the kids in Twinkle Elementary; Ninten coming home to be greeted by his family; Ana reading a letter given to her by Ninten; and Ninten taking a nap as all of the characters you've encountered in the game run by, ending with Ninten, Loid, Ana, and Teddy walking up and facing the screen. And then the credits roll, ending with Ninten's dad calling on the phone.
At the end of Neverwinter Nights 2, the player is shown what happens to various locations and people who were influenced by the PC's decisions. For the ending itself, though, there are only two options. A good or neutral PC defeats the King of Shadows, then everyone dies. An evil PC may instead choose to side with the King of Shadows and terrorize the Sword Coast, though the sequel assumes that the player picked the good ending.
The sequel/expansion pack provides a far more interesting array of different endings concerning both the PC's fate and that of his/her companions. For example, if you gathered all the Mask Fragments, you can get the ultimate good ending and put Akachi's soul to rest while also freeing yourself and the land of the curse. Regardless of whether you have the mask pieces, you can choose the selfish ending and rid yourself of the curse, but leave it free to continue plaguing Rashemen. If you failed to collect the Mask Fragments, you may choose the completely selfless ending, locking the curse inside yourself and eternally staying in the City of Judgment to contain it, praised as a hero, but forever trapped. Or, there's the ultra evil approach; bending the curse to your will to become an unstoppable god-killing abomination with all of the benefits of the curse but none of the drawbacks. Similarly, the endings for your companions vary depending on both your choices in the game and the actual influence with them. For example, if you've pursued a romance, your beloved may choose to stay with you in the City of Judgment in the selfless scenario. At the other end of the spectrum, you may reach the end of the story with all of your companions dead by your hand.
The second expansion "Storm of Zehir" has a similar conclusion if you've played the main quest to the end, showing the fates of your companions and the towns you visited according to your actions. Unusually, after seeing this, you can Bluff or Intimidate the storyteller into giving the different endings by telling him how to set each variable. This even extends to companions you never actually recruited (or even encountered, since several are found randomly wandering the world map) and side-quests you never found out about.
In Sailor Moon: Another Story, there are two endings that will play out depending on how you defeat Apsu, who has fused with Sin the second time you fight her:
If you beat her with Sailor Moon's team, Sailor Moon will use the Silver Crystal to finish her off, and get Sin to do a Heel-Face Turn like her brother Anshar and the other Oppositio Senshi have. Anshar will then give Chibi-Moon the pendant she accidentally lost on the day they first met and they'll kiss. The Sailor Senshi, Tuxedo Kamen, Luna, and Artemis go back to the present, Hotaru turns back into an infant, and everyone goes home.
If Sailor Moon's team falls, it's up to Chibi-Moon's team, but... with her last bit of strength, Apsu tries to attack Chibi-Moon, but Anshar saves her and tries to convince his sister Sin that she's not evil. Once Sin snaps out of it, Luna tells Chibi-Moon to use the Silver Crystal, but the fates of Chibi-Moon and Anshar will change, and she isn't happy about this because they loved each other. And then, the next day, Chibi-Usa bumps into Anshar again like when they first met. Due to his fate being altered, Anshar doesn't remember Chibi-Usa, and neither does Sin. Chibi-Usa asks Setsuna if it's right to leave Anshar alone, and Setsuna says it is because it is fate. Chibi-Usa accepts this, and says that she'll never forget him and she loves him.
The first Baldur's Gate and Shadows of Amn only have one ending, but the expansion to the second game that concludes the story has three main endings (Good God, Bad God, and Mortal) as well as side-endings for your various companions.
In Fable, you can play as good or evil. However, in both the original and the "Lost Chapters" expansion, the choice of the "good" ending or the "evil" ending is a conscious decision made by the player between when the final boss is killed and when the ending movie starts.
Fable II is odd in that although it leaves almost every other choice throughout the game ambiguous, it makes the Evil ending for the original game, and the Good ending for the Lost Chapters segment canon.
Fable II's ending sequence actually lacks a "good" or "evil" choice. Regardless of your goodness or evilness, you kill the guy you've been after for the entire game, either out of revenge (evil) or to save the world (good), and that's only implied. But, afterwards, you get the option of making a wish, and can choose to either revive everyone that died in the Big Bad's evil scheme (the "good" choice), you can choose to revive your family and dog (the "neutral" choice), or you can wish for more money than you know what to do with (the "evil" choice). All choices have little effect on the world at large. Instead, the major world changes result entirely from your choices in the game: Old Town can be either pristine or a slum, the Temple of Light can flourish or be abandoned, and so on.
Fable also has the flaw of your goodness and evilness being highly influenced by armour and clothing. One can easily switch back and forth by literally changing clothes (in fact, it is the only real way, as a good character in good clothing will have a very hard time becoming evil, even by slaughtering entire villages).
For example, in the SNES version of the second game, Der Langrisser, there are four basic story paths: Light, Imperial, Chaos, and Independent, each involving on the main character Erwin joining one of three factions (the Light Army of Kalxath, the Rayguard Empire, or the forces of Chaos) or turning his back on all three, each featuring a different roster of playable allies (most of whom can also be enemy characters on other paths), and each leading to a different epilogue.
Even within each of the four possible story paths, there are dozens, if not hundreds, of possible permutations of epilogues for the characters involved. The individual character epilogues depend on whether the characters reached their highest class change, how many enemy units they killed, how many times they were reduced to 0 HP, and so on — if they were particularly active in the battles, they go on to greatness throughout their lives, whereas if they were frequently reduced to 0 HP or sat at the back and did nothing, they fade into obscurity after the events of the game.
All three games in the Shadow Hearts series do this. Shadow Hearts has it based on whether you manage to beat a series of side bosses, which is nearly impossible unless you do it in the right order, although this order is provided on an item you get in the game. Oddly, Shadow Hearts: Covenant was actually based on the "bad" ending of the original, not because the good ending is terribly hard to get, but because it fits the tone of the series better. Of course, many of the fans disagreed. Shadow Hearts: From The New World was based on whether or not Tirawa's statues were fully leveled up.
Oddly, the ending you get in Shadow Hearts: Covenant is not determined at all by your playing ability or uncovering secrets, but the way you answer a single question toward the end of the game. It can be argued that what this actually tests is how well the player understands Yuri's character, as picking the less in-character response will net you the bad ending (although which answer is really more in-character is quite debatable.)
Also unique in that the good ending is the one where you die, and the bad ending is the one where you live. But it makes perfect sense in the story's context.
The prequel, Koudelka, has three endings. The really bad ending happens if you didn't pick up a certain item over the course of the game; the final boss kills everyone as soon as they enter the last area. You get the meh ending if you beat the final boss. And you get the "good" ending if you lose to the final boss — which is way harder and more time consuming than winning.
Deus Ex had three possible endings, none unambiguously "good", determined by which faction the player character chooses to support in the end. The sequel had a compromise setting based on the idea that all three factions had managed to achieve their goals, with or without the player character's help.
Game ModThe Nameless Mod had six endings. Only two are availble on any story line, the rest depending on what faction you supported.
Another mod, 2027, had three endings, which may or may not all be available depending on choices you made throughout the game.
Deus Ex: Invisible War had four endings for four parties. One could argue nuclear winter, or starting a genocidal, technophobic, fascist regime are the bad endings, the other two force their idea of a perfect society on the world. Thus, while the original created three endings, each with a bit of hope for a brighter tomorrow.
And then there's the hidden Dance Club ending, which you can reach by flushing a toilet in the final level while carrying a flag.
Deus Ex: Human Revolution had four endings chosen by a push of a button that would explain to the world why the augmented population was going insane, or one that would kill yourself and everyone aboard the station you were on. Interestingly, The Stinger shows that, no matter what you did, the original Deus Ex will happen.
Jade Empire did most of the above for well over 20 variations on its ending. It had different endings based on your Karma Meter, the romantic relationships between yourself and your followers, and their Karma meters as well. It also had hidden pasts for two characters resulting in about three or four different endings per follower on top of the three main endings for your own alignment (Good/Evil/Dead/In Love With Hero/Secret Past/Secret past and In love with Hero/Evil with a secret past whilst in love with the hero... and you get the idea). These epilogues were only played after the main ending cutscene, however, which was chosen from 3 possibilities depending on whether the main character was good/evil/an idiot.
Live A Live has no less than four endings, three of which are bad, and two versions of the good one. (The second bad one is triggered by the best battle choice box in gaming history: Fight / Pass / Item / Armageddon.)
Recent games in the Fire Emblem series have a feature called "support", in which characters that spend a lot of time together in battle can have conversations which increase each of the supported characters' stats when they're near each other in battle. Certain preset supports change the ending, with the supported characters getting married and having children, and supports for the main characters will get an extra scene in the ending.
Contrasting this, if you let characters die during your playthrough, at the end of the game when you would hear about how they went on with their life, you get a "Character died during Chapter" message for unimportant cast members or "Character critically wounded during Chapter" message for main characters that aren't the Hero.
Path of Radiance and Radiant Dawn have multiple endings as well, depending on whether Ike defeated the Black Knight or not in the first case, and a whole bunch of different factors in the second case. For example:
Whether you killed Pelleas or not
Whether Soren ever fought Micaiah and Pelleas or not
Whether you killed Lehran or not
Also, Fire Emblem: Sword of Seals has three possible endings: the standard ending, the complete ending, and the best ending. The standard ending can be obtained by simply defeating Zephiel. If all the sacred weapons have been obtained, two extra chapters are unlocked, leading to the complete ending, in which you defeat the dark priestess Idoun. The best ending occurs if Idoun is finished off by Roy using the Sword of Seals, and it shows Idoun's soul being saved.
Fire Emblem Awakening has two endings based on a choice in the final chapter. The Avatar can choose to sacrifice him/herself to destroy Grima for good, or have Chrom kill Grima but have Grima come back again in the future.
Not that it matters, since the Avatar comes back to life while Grima remains dead forever if the player chooses to sacrifice the Avatar.
Mystery of the Emblem and its remake have two endings, one bad and one good. If you manage to collect all five orbs (one of which is in twelve pieces), the binding shield will be completed, and dispel the illusion that Gharnef and his followers use to disguise themselves as the clerics that they had kidnapped. This will unlock four more chapters where Marth and crew travel to the heart of the Dragon's Alter, where Medeus has been revived. Failing to this will cause Marth to fall for Gharnef's disguise and think the day is saved, allowing the Earth Dragons to awaken and cause the end of the world.
FInal Fantasy XIII-2 is a bit weird. There are eight "Paradox Endings," most of which are bittersweet (and one of them is just weird). There is also a Secret Ending obtained after getting all 160 fragments, in which Caius taunts the player by telling them that all possible timelines lead to him winning.
Notable in that one quest results in a bad ending, no matter how you completed it. Mephisto offers you a Sadistic Choice between saving Jean Grey or Nightcrawler. Saving Jean results in Mystique murdering Charles Xavier for allowing her son to die, whereas choosing Nightcrawler causes Dark Phoenix to escape hell and come to seek revenge on the X-Men for abandoning Jean.
The PlayStation 2 game Shadow Of Destiny had five different endings (actually six — two of them have the same ultimate result, but achieve it in different ways), determined by the choices you made at certain junctures and whether or not you'd witnessed certain missable events. Each ending filled in different details of the overarcing plot, so it was necessary to play to all five of them to get the full picture of what was going on. Upon having seen all five of the endings, a new sixth (seventh) ending became available.
There are actually two extra endings, one is the happiest possible ending and one is happy but leaves some unresolved issues. The first involves the hero helping create the Elixer of Life instead of releasing Homunculus, thereby healing Dr. Wagner's wife. The other ending involves removing the Homunculus from existence via a temporal paradox, but Dr. Wagner doesn't get to heal his wife. Both endings still achieve a similar result: without Homunculus setting his plans into motion, underlying reasons of the story never come to pass, and Eike no longer exists because Wagner never wished for eternal youth.
The Elder Scrolls series managed to dodge the need to stick with just one ending for the plot with Daggerfall, by later stating that the reality-warping powers of the Numidium that everyone was fighting for made all the endings happen, with two possible exceptions (it remains unclear whether the Underking earned the death that he sought, and in-game sources suggest intervention by divine agents made the King of Worms at least not entirely a god). On the other hand, Sentinel, Daggerfall, Wayrest, and Orsinium all simultaneously expanded over the smaller territories of the Iliac Bay region, while the Empire ended up with more control over the four newly-formed counties than it possessed when the region was more divided.
The Guardian Heroes series managed to dodge the need to, as well. This time, not by choosing all of the endings, but none of them. The "ending" that's the kick-off for Advance Guardian Heroes is loosely based on one of the endings from the first game, but redoes it as a bad ending; a variation that doesn't exist in the original game, which simply doesn't have any bad endings, just several, very different good ones.
In the first Star Oean, the way the main character reacts with the other characters affects his Relationship Values with them, which in turn affect the way the story unfolds and which of the the Multiple Endings the player gets.
Star Ocean: The Second Story has 87 ending sequences that are primarily used as resolution and are determined by how the various characters relate to each other. Because you have up to 8 characters, you will see 4-8 of these sequences during the endings (depending on how many characters are paired up with others). In addition, the beginning of the game gives the player the option of choosing to play as either Claude or Rena (the two protagonists) giving a different point-of-view for each choice.
For a linear tactical RPG, Fallout Tactics probably did pretty well with no less than four endings, not counting if the main character dies:
The 'standard' ending: The player destroys the Calculator. The Brotherhood struggles in the following years, but survives and eventually prevails.
The 'good' ending: A character who has made mostly moral choices merges with the Calculator. The Brotherhood prospers under their benevolent hand, and so too does the Wasteland.
The 'evil' ending: An immoral or... pragmatic character merges with the Calculator. Together, they create a feared, but fair and efficient, police state, ruled solely by the Calculator's ruthless mind.
The 'what the hell?' ending: General Barnaky merges with the Calculator. The Brotherhood is made more powerful, but mutants and ghouls are discriminated against, until a rebellion of both oppressed mutants and ghouls and sympathetic humans rises against the Brotherhood. It is doomed to fail. The Brotherhood survives, as does the player character.
The Breath of Fire video game series tends to have a "main" ending and several "secret" endings. The first game has an extra (bad) ending where you defeat the final boss without revealing her true form first. The second game not only has a bad ending, it has a "best" ending which relies on an earlier boss fight. The third game also has a bad ending, and the fourth game lets you side with the villain and fight your former party members.
The Geneforge series of games by Spiderweb does this pretty well. For each game, there are at least half a dozen different endings, depending on which faction you completed the main quests for, who you betrayed or killed, and various other actions through the course of the game (such as how many crazy-inducing augmentation canisters you used). However, there's only one canon ending per game, since the next game has to have a definite starting point.
The first three somewhat glossed it over, leaving the assumption that the choice made at the end of the previous games weren't so relevant to the beginning of each game. The last considered the 'stalemate' ending of the fourth to be canon, a compromise which also happened to be a fan favorite.
Also note that this is one of the games where most of the endings suck. For instance, in the first game, your only chance at a traditional "good" ending is to kill the villain and destroy the Geneforgewithout ever using a canister. Alternately, you can use canisters, but destroy the Geneforge anyway. Your people will be saved, but the canisters permanently mark you as no longer fully human, and you're left financially rewarded but rejected and friendless. A couple of the other endings allow for your personal survival at the expense of your entire society, and most of the rest kill you and lead to a bloody war.
Planescape: Torment has five endings, ranging from bittersweet to downright depressing. The main effect — the immortal player character finds out how to die — is retained for all of them; the rest of it mostly deals with what happens with him afterwards, and if your NPC friends survive.
Not to mention the Non-Standard Game Over endings — one of which involves you accepting the position of Silent King once the advisor knows that you know he's dead — since this is a lifetime appointment, and you're immortal...
Interesting that it had a Screw This, I'm Outta Here! ending, because the lack of save games resulted in more than a few players choosing such an ending theirselves, rather than finish the thing.
Mass Effect has three endings, with a minor variation depending on which ending you chose and whether your Paragon or Renegade meter is higher. If you save the Council, humanity is given a seat on the council with either Anderson or Udina as the representative of Earth. If you deliberately let the Council die, humanity becomes the sole species of the Council, with either Anderson or Udina as Chairman, and if you choose to concentrate on Sovereign, which leads to the Council's death, your ending will be decided by your Karma Meter: If more Paragon, humanity will establish a new Council, with a human Chairman (either Anderson or Udina) leading a multi-species Council. If a Renegade, Udina will use your ruthlessness to lead humanity into ruling the galaxy with an entirely human Council.
Mass Effect 2 has a few dialogue changes based on how you played the first one, and minor characters reappear.
Being a game with a heavy emphasis on player choice, even the dungeons in Mass Effect 1 can have slightly different endings depending on what order you tackle them in and the choices you make in each dungeon. A good example is in Noveria, where the boss fight with Matriarch Benezia will play out slightly differently depending on whether or not you have Liara T'soni in your party, whether your brought her along with you, and whether or not you choose to save or wipe out the rachni. You also get an extra cutscene if you bring Wrex and decide to save the rachni, where he chews you out for saving an obviously evil bug race that the krogan dedicated themselves to wiping out years ago. And all that is just in the final act of one dungeon. Let's not get started on Virmire...
The ending of ME2 can literally range anywhere from Everybody's Dead, Dave to the Golden Ending due to the absolutely deadly nature of the suicide mission. In addition, there's keeping the Collector Base or not, sticking with Cerberus or not, the implications of not doing certain loyalty missions, particularly Samara's which has your ending leave an immoral serial killer on the loose, etc. Let's face it, the Mass Effect series and its game importing power take multiple endings Serial Escalation.
Interestingly, No Canon for the Wicked could be considered to be inverted — if you start a new character in Mass Effect 2, he/she will have made all the bad choices (Wrex died, the council died, Shepard chose Udina rather than Anderson, the Rachni were wiped out — the only highly significant one that may turn out 'as expected' is that Shepard will save Kaiden if female and Ashley if male). This led to many people starting from Mass Effect 2 to either import someone else's character with the desired decisions, or use a save editor to create the character they want. As discussed on Cutting Off The Branches, some fans speculate this is a sneaky way of encouraging players to play the first game instead of jumping into the sequel blind. On the other hand, the PS3 version, due to the first game never being released for that system, includes an interactive comic book that allows the players to make decisions about major events.
Mass Effect 3 has three choices for the ending, with the choices available and aftermath of the final battle varying depending on the player's Effective Military Strength rating. Ultimately, the choice comes down to annihilating the Reapers along with all other synthetic life in the galaxy, uploading your mind into the Reaper fleet and controlling them, or fusing organics and synthetics into a new hybrid-form. The aftermath of each choice is similar: the mass relay network is damaged, and the Normandy crashes on a jungle planet. The fourth option, Refusal, has Shepard ignore the superweapon, and causes the Reapers to win, exterminating all the sentient species in the galaxy. However, several caches of information survive and allow the next cycle of sentient life to fight the Reapers and win.. Your moral choices affect the outcome of each choice, such as a Renegade Shepard taking the Control ending, resulting in him setting himself up effectively as a god-like dictator, as does your Effective Military Strength; having too little EMS will result in the Crucible misfiring, causing a fireball that kills all Reapers, but also effectively destroys all life on Earth, and most of the starships in the galaxy.
Dragon Age: Origins – Awakening had two endings, but with major variations: "Amaranthine's Last Hope" (the Warden-Commander saves the city of Amaranthine from Darkspawn, but the Vigil's Keep is destroyed) and "Keeper of the Vigil" (the Warden-Commander saves the Keep, but Amaranthine is burned to the ground). One variation was that combining the first ending with the "Enduring Vigil" Achievement meant that neither the city, nor the fortress ever fell, making it the Golden Ending. The second variation was whether the Architect is killed or spared.
Dragon Age II has two endings: Mage (Hawke sides with the mages, starts a revolution, and skips town), and Templar (Hawke sides with the Templars, crushes the Kirkwall mage rebellion, and is crowned Viscount). Regardless of your choices, however, the overall outcome of the game is always an all-out war between Mages and Templars across Thedas no later than three years after the ending, and Hawke ultimately disappearing (with love interest, if there was one).
Lands of Lore II had a Good ending and an Evil ending, depending on choices the player makes in the game. This game is one of the few cases where the Evil path is actually preferable — it allows you to skip one of the most difficult and annoying parts of the game.
Technically there's a good ending and a bad ending, with several different bonus cutscenes added to the bad ending depending on choices the player makes at the end of the game. Getting both endings and all the bad ending cutscenes is required to unlock the True Ending.
Valkyrie Profile is a bit odd. It's possible (but not easy) to get a standard Game Over. You can get the "C" ending by directly working against the instructions you're given, and the "B" ending by following them. But in the absence of a guide, I challenge you to get the "A" ending. Hell, I challenge you to prove that the "B" ending isn't the "A" ending!
Odds are good that there are players who figured it out on their own through sheer testing and playtime, just because the "B" ending is so completely unsatisfying.
The second game left out multiple endings, but the third game brought them back in, with your ending dependent on how often and how much you used the Destiny Plume. Spamming the Plume too much results in the worst ending, where you get your ass whipped by Freya, while not using it at all in the entire game (save for the one in the tutorial) results in the best ending, where you fight Hel's hound, and obliterate it, saving your own soul. You need to get all but the worst ending in order to enter the SeraphicGate.
Like Indiana Jones and the Fate of Atlantis, Front Mission 3 had multiple completely different paths through the game, specifically two. And like Fate of Atlantis, the branching point was absurdly well-hidden, hinging entirely on whether or not you chose to go to a certain location during the prologue segment.
Vandal Hearts II has six different endings (two of which were minor variations on two of the others). Only one really counted as the "good ending", and acquiring it definitely came under Guide Dang It territory.
The first game has two different endings, and it's difficult to tell which one is officially canon. The standard ending for beating the game shows Aya and her friends watching the play from the game's start, when everyone in the audience gets glowing pink eyes, due to the mitochondria acting up. Aya rises up from her seat and the camera cuts to the stage to show the whole audience with glowing eyes. The alternate ending is obtained when you beat the Bonus Boss, which shows Aya reverting back to normal (losing her powers) and just walking away.
Parasite Eve 2 has three different endings based on what events you trigger during the game. The standard ending shows a black screen with the President talking to his aide over the events of the end of the game. The good ending shows an extended version of this with the President and his aide in the picture as they also discuss on what to do with the mole they sent. The best ending shows various artworks of the characters and what has happened to each one of them. After the credits here, Eve and Aya visit the Museum of Natural History to see some exhibits when they see a mysterious figure near the doors behind them. It is presumed to be Kyle.
Sweet Home has five endings. The ending you get is determined by how many members of your group are still alive at the end. The 'best ending' is actually a The End... Or Is It? ending, while the rest are more bittersweet than downers.
Dark Messiah of Might and Magic has four endings, the one you get based on two forks. The obvious one is at the very end of the game, where you decide what to do with the Skull of Shadows, but the not-so-obvious one is tied to two optional quests; failing/neglecting to do either one locks you into one pair of endings (presumably the bad endings), but doing both gets you a different pair of endings and the ability (skills pending) to use +7 Holy-Attributed Weapons (which will pretty much be your weapons of choice for the remainder of the game). The catch? You lose Xana and your demon form.
Might and Magic VII had two, based on a mid-game choice. The good ending, in which the colony's connection to an interstellar Portal Network is repaired was probably canon, but the evil ending, in which the Heavenly Forge is repaired, allowing the evil guys — which include your group — to outfit their armies with blasters and other technological wonderswas intended to be canon, before backlash amongst part of the fandom made the developers alter their previous plans for Armageddon's Blade.
Incidentally, the Law and Chaos endings in Shin Megami Tensei I both suck royally, and the neutral one isn't much better. This has since become a hallmark of the series.
Shin Megami Tensei Nocturne has 5 endings selected upon your actions before entering the final dungeon, based on who you've allied with, and in the US version whether or not you completed the bonus dungeon prior to entering. This actually affects more than just the ending, as it also affects the bosses you'll need to fight. There are total of 4 bosses you can fight in the final dungeon, but depending on your actions, you might be able to skip one of them.
If you allied with Chiaki, then you'll still have to fight her, due to her "strong rules all" philosophy, as well as Isamu and Hikawa before facing the final boss.
If you allied with Isamu, he'll be defeated prior to entering, so you won't have to fight him; however, you'll have to fight Chiaki and Hikawa and then fight the final boss.
If you allied with Hikawa, he'll allow you to pass without fighting him, but you'll need to fight Chiaki and Isamu before fighting the final boss.
If you allied with none of them (by either rejecting all of them or trying to ally with more than one of them), then you'll have to fight all three of them. Also, the ending you get depends on how you responded to a certain character's questions earlier. If you responded with fear, then you won't fight the final boss, and you'll get the worst ending where nothing changes.
If you do the above but answered with courage, then you'll also fight the final boss and upon winning get the good freedom ending.
If you completed the Amala Labrynth and became a full demon, then you'll be forced out of any alliance you may have had and need to fight Chiaki, Isamu, and Hikawa as well as the original final boss. After that, you'll need to fight a new final boss after the original one.
In Shin Megami Tensei If, the type of ending that you get is decided by which character you picked as a partner in the beginning of the game.
Shin Megami Tensei IV also has a Law, Neutral, and Chaos ending in addition to a fourth ending unlocked by making a certain choice near the end of the game.
The original Persona has four endings: a good and a bad ending for both the normal plot and the Snow Queen Quest.
Normal Path: Which ending you get depends on whether or not you answer certain questions correctly. Get any of said questions wrong, and you get a bad ending at the moment of the revelation. Get them all right, and the game continues to the final boss and Good Ending.
Snow Queen Quest: The only way to get the bad ending is to try to proceed past a certain point in the game without having enough of the mirror shards picked up throughout the game. Since most players would most likely try to get all the mirror shards, this can be difficult. Naturally, the good ending happens if you do get enough mirror shards.
Persona 3 forces the player to make a difficult choice: it turns out your friend Ryoji is the unwilling harbinger of the Big Bad, Nyx, who he claims is totally unstoppable. Ryoji offers to let you kill him, saying that if you do this before midnight on New Year's Eve, your memories of the impending apocalypse will be erased and you can live out what little time you have left free from the painful burden of knowing the end of humanity is coming. If you choose to kill him, your characters get to live three months as ordinary high school students without a care in the world. The final shot is of you happily and unknowingly singing karaoke with friends, a split second before Nyx wipes out all life on Earth. Choose not to kill him, and the game continues on into January, leading up to an eventual confrontation between your party and Nyx.
The bad ending may also count as a Nonstandard Game Over, since this choice does NOT happen at the end of the game. If you choose not to kill Ryoji, the game will continue for a while longer.
Persona 4's multiple endings were designed, clearly, by a true sadist, and operate like peeling the layers off of an onion: First you get the standard-type moral choice you get in most multiple endings. Get revenge by murdering the murderer, or hand him over to the police, knowing he won't be convicted. The best choice is to stall for time, because he's not actually the murderer. The third bad ending can be avoided only if you can guess the true murderer in three tries, with very little evidence. The second-best ending then tries its damndest to convince you that it's actually the best ending possible. Only a series of totally counterintuitive actions will lead you to the true puppetmaster, the true final battle, and the real best ending.
The remake adds another ending that is one huge What the Hell, Player?: You become the murderer's accomplice and destroy incriminating evidence. It also adds an extra epilogue if you achieve the true ending and complete a certain bonus dungeon.
Devil Survivor has five main endings, most of which hinge on what the player decides how to handle the threat of demons, and who to align with. With varying results. Note that it is easier to categorize some of the endings by the standard Law/Chaos alignment of SMT rather than Good/Bad. To elaborate:
Chaos: You become demon overlord by teaming up with Naoya/Cain and/or Kaido, and proceed to fight God, while humanity huddles in a corner avoiding all conflict. Humanity is free but is constantly under threat of annihilation.
Law: You become the world's messiah by joining Amane, and have the Demons serve God, and kill anyone who opposes your system. Humanity is preserved but all freedom is taken away.
Neutral (Song of Hope): You send ALL demons back to where they came from with Haru's song, giving up the power of Bel but freeing humanity from supernatural threats forever. This is the most difficult ending to acquire and survive, through.
Neutral (Silent Revolution): You manage to control all of the demons with the Server with Atsuro's hacking, causing a new technological revolution that turns Japan into a superpower.
Bad (And the one you can get by default): You run away by listening to Yuzu's (poor) advice, and by doing so get the whole world killed. "What you found outside was no different from what you ran away from. And the only angels that could have stopped this were killed by your own hands."
The Overclocked remake adds an extra day to three of these endings, allowing for a more detailed ending which, against SMT tradition, are pretty much positive.
Chaos/Good: You refuse to kill any humans as you drive out the angels, sending them back to heaven after defeating Metatron. You then head to the demon world alone to raise an army against God. Notable in that it is the only ending where you can get all 10 potential party members.
Chaos/Evil: You cut down everyone who stands in your way and drive the angels out. Before raising your army against God, you use your demons to subjugate humanity to become the ruler of two worlds. In the process, you lose all your friends except for Naoya, Kaido, and a corrupted and broken Atsuro.
Law: You start enforcing the will of God, and in the process can prove to God that even people He (or his angels) declares irredeemable can actually be redeemed. You then stop Japan's creator god from destroying Japan by showing him Cain has changed slightly, and in the process you set Naoya/Cain on the path to potential redemption (though he'll never side with God since he manipulated him into killing Abel).
Less Bad/Neutral: You escape from the lockdown, finding out that your families have been captured by the government, and angels are starting to try and assert control over mankind. Wanting to fix everything, you head back into the lockdown where you defeat Belberith to potentially stop the influx of demons, and (optionally) help the Devas restore the barrier between the human and demon worlds. You essentially spend the rest of your life helping fix the mess, but if you fail to restore the barrier, then demon attacks stay a regular occurrence within Tokyo.
Bad Neutral: You fail to do the barrier events or Gin being dead during that playthrough means that demons will continuously flood the earth at the end with no way to close it. It's also the only one that doesn't earn any achievements for getting it.
Devil Survivor 2, following the first game, also offers five endings and one Golden Ending. These are different as they are based upon the Qualities of a Star Sign instead of on alignments. Upon and after fighting the Final Boss who's been trying to destroy the world:
Cardinal (Law): Also known as the Egalitarian ending. You ally with Ronaldo Kuriki and convince Polaris to bring a world of equality, where everybody works for the benefit of everyone.
Mutable (Chaos): Also known as the Meritorious ending. You ally with Yamato Hotsuin and convince Polaris to bring a world ruled with meritocracy (a mild case of Social Darwinism), where those with skills and talents prosper and the rest are weeded out.
Neutral: Also known as the Restorer ending. You ally with Daichi and convince Polaris to restore the world, bringing you back to the time before the events of the game start, i.e. pressing the Reset Button. It concludes with a message asking whether or not Polaris will just destroy Earth again.
Fixed: Also known as the Liberator ending. You ally with Daichi and decide to kill Polaris, freeing humanity from its control and threat but also leaving you with a world already badly ravaged by Polaris (the void isn't undone, leaving only Tokyo and a sea full of undrinkable water). You also removed any supernatural influence and pretty much doom what's left of humanity to slowly starve to death. For some reason, the game treats this as a good thing.
Neutral/Chaos: Also known as the Kingmaker ending. You ally with Al Saiduq and decide to kill Polaris and have Al Saiduq replace it as the world's god and create a new world.
Fixed+: Also known as the Triumphant Restorer ending. You ally with Daichi and convince Polaris to restore the world, identically to the normal Restorer ending. The difference is that, having recruited every party member and made them all grow and develop, this development shines through in the restored world. The message at the end states that Polaris definitely will not just destroy Earth again.
Tales of Symphonia: Dawn of the New World has 3 endings: The Best Ending, The Good Ending, and the Bad Ending. You get the Best Ending by getting both Ignus' and Tonitrus' Cores and losing to Lloyd and Marta and involves Emil splitting from Ratatosk and returning to Earth to live a normal life. You get the Good Ending by losing Ignus and/or Tonitrus to Lloyd and involves Emil/Ratatosk and Richter staying in the Ginnungagap. You get the Bad ending by winning the fight against Lloyd and Marta and involves Emil killing himself because he injured Marta. The Bad Ending is pretty much a Nonstandard Game Over.
Girls Love RPG Embric of Wulfhammer's Castle is built on its multiple endings, most of them implying different truths about the world setting and the actual events of the narrative; unique in that getting most endings doesn't actually end the game — the credits roll, but the player can choose to return to the point just before the last ending they got. Characters lampshade this, and at one point someone says she doesn't accept anything as being true unless she encounters it three times.
The sequel's primary ending changes depend on who the player sided with in the first act, Roche of Iorveth, and whether Geralt decides to help his ally or go save Triss in the Third act.
Radiant Historia plays with this interestingly. In most of the "Nodes" in each of the two histories, it is possible, through certain actions (some less obvious than others), to screw things up so badly that you get "treated" to a (oftentimes horrific and/or tragic) BAD END before being booted to the previous Node to try again. The final ending will also change depending on which sidequests were completed.
Venetica has two endings depending whether Scarlett, through dialogue options, fought for either revenge (good ending) or personal power (bad ending).
The Ar tonelico series has this, partially owing to its Dating Sim hybrid nature. For instance, the first game has seven endings based on which girl you choose and certain choices that will end the game early.
Hanako Games specializes in multiple endings. Cute Knight and its sequel Cute Knight Kingdom have twenty or thirty endings apiece, mostly depending on your job, sin level and the amount of adventuring you did, although there are a couple of "special endings" like marrying a prince or becoming a mermaid. Charm School has about twenty different endings for each of the three main characters, depending on which classes they took and whether they had a good or bad attitude at the end of the game. Magical Diary - Horse Hall has five or six major endings to your year at wizard school, and they've also got several visual novels.
Long Live the Queen, also made by Hanako Games, has over a dozen bad endings depicting the princess' demise ranging from swords and arrows to poisoned chocolate. It only has one good end where Elodie gets crowned queen. However, depending on the many choices and possible ways to reach coronation, pictures styled like stained glass describe what happened afterwards. Some are heart-warming and some are delightfully evil.
I Miss the Sunrise has two endings, called "optimist" and "pessimist". The former involves fighting the Big Bad, the latter involves siding with them.
Eternal Sonata has two endings, If you beat Chopin, he dies in his dream and real life, Polka seemingly kills herself, and is reborn, but then comes back to life with Frederic. And the bad ending? Just lose against Chopin, and he wakes up from his dream, then he closes his eyes again.