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The Legacy of Kain games deal with the attempts of the immortal vampire Kain to change his fate and that of the world of Nosgoth, which are tied. Frequent use of time travel is made by Kain, Raziel, and Mobius the Timestreamer to advance their own agendas. For example: Mobius traveled back in time in the first chapter of the series "Blood Omen" and corrupted the King William the Just, turning him into The Nemesis, who threatened to conquer all of Nosgoth in the future. Kain inadvertently travels back to this time period, where he kills William the Just before he manages to become The Nemesis. When he returns to the present, Kain realizes that by killing William the Just he has sparked a genocide against vampires that left him the last in all of Nosgoth.
Then it gets revealed that changing things through time travel is really In Spite of a Nail... unless one triggers a paradox by having the same person/thing at the same point in space/time twice. Kain's battle with William the Just was such a paradox because they were both wielding the Soul Reaver. Later on, Raziel becomes a walking paradox when he absorbs the spirit of the Soul Reaver, which is his own soul from a later point in time. From that point onward, there are always two of him wherever he goes, so he can change the timeline as he wills. Unfortunately, he's rather easily manipulated, making his status as the only person in Nozgoth with free will a moot point.
One of the drama CDs based on Guilty Gear revolves around an Alternate Universe in which the war lasted ten years longer because Ky Kiske was killed in the penultimate battle, and in which the Gears would have won if I-No hadn't gone back in time to rescue him.
Chrono Cross features the death of its protagonist as its nail. This seemingly meaningless event changes entire worlds, though, as, for example, one character that's dirt-poor in one world is filthy rich in another. His family still resents him in either timeline though.
Technically, he resents his family. And that's not the strangest difference, either. Consider the twin sisters that were never together. Ever. In fact, they shouldn't even be twins! Huh?!
This one is weird and complex and involves numerous time travel and alternate universe tropes besides just the one relevant, but the short version is that most of the changes actually depend on the existence or nonexistence of the supercomputer FATE, but this itself depends on the death of its protagonist.
The two spinoff games to Scarface (1983), The World Is Yours and Money. Power. Respect., are based on Tony escaping the film-ending shootout, while the comic Scarred for Life is based on Tony surviving wounds that were fatal in said shootout. Tony's survival either way is a small but very important difference, with above scenarios being impossible "normally".
The original Mega Man series and four of its spinoffs have focused on Dr. Light's aptitude for robotics and the battles his creations have fought in the process of trying to keep a rival from taking over the world. However, Dr. Light focusing on internet technology instead of robotics results in the Alternate UniverseBattle Network and Star Force spinoffs. Wily is still a roboticist, however; his actions start out as revenge against society for pushing the field of robotics aside.
Chrono Trigger features a scene where Marle, sent into the past, is mistaken for the missing queen Leene; they call off the search, meaning that the real queen stays missing and is presumably killed. This has the unfortunate effect of causing her present-day descendant, Marle, to cease to exist. The part is notable because later timeline changes don't suffer the same "paradox correction"; for instance, you can raid the Black Omen in one era, then travel back and raid it in an earlier era, and still keep the spoils from the previous raids (though if you raid it in one era and then try again in a later era, everything will already be gone). Apparently they had different writers with different ideas.
Word of God says that the team hadn't worked out the rules for time travel until after they'd painted themselves into a corner with that plot point.
Fan Theory can patch the Plot Hole if you assume that traveling to the End of Time, a place where time doesn't exist or is distorted/frozen, grants you time-traveler's immunity.
In Resistance: Fall of Man, Europe comes off prosperous and peaceful after WWI, preventing the Second World War. However, instead of a Revolution, aliens invade Siberia. Russia can't catch a break, can it?
This is a major plot point in Dark Chronicle. Emperor Griffon has destroyed the "orgin point" of several important places, which Max and Monica have to fix.
The Fallout series revolves around this trope: slight changes in the direction of politics and technology after the end of WWII resulted in a completely different world just a few decades after, and ended turning the world into an apocalyptic wasteland.
Indeed, in Fallout 2 the player can go through the time-portal from The City on the Edge of Forever from the original Star Trek. The player ends up in (spoilers) Vault 13. If he taps a computer, it sets up a water chip to fail, which will end up causing...
Discussed in Magical Girl Lyrical Nanoha As Portable: The Battle of Aces, where it is suggested that Fate would have turned out like the Ax-CrazyBerserker Material-L if she had never met Nanoha or the others. Nanoha disagrees with this suggestion though, noting that Fate is a stronger person than that, and that with Arf, she is not truly alone.
Duncan serves as the nail in Dragon Age: Origins and its various Origin stories; his presence in the events of any given origin determines whether the character associated with that origin goes on to become the hero of the game's story.
If Duncan isn't in Highever when Arl Rendon Howe betrays and attacks the Couslands, the youngest Cousland doesn't manage to escape the castle and dies with the rest of the family (as presented in the Human Noble origin the youngest Cousland could very well have escaped the castle — but the other origins indicate the Cousland's death, and even if the Cousland got out of the castle he or she would have been alone, hunted and with a less clear destination without Duncan's assistance).
The Dwarf Commoner is unable to escape the Carta's prison and ultimately dies of starvation without Duncan's intervention.
The City Elf is either murdered by Bann Vaughn or dies in the ensuing riots in the alienage if Duncan is not there to lend weapons to him (or Soris, if the PC is female) or invoke right of conscription to save the PC from arrest.
The Dalish Elf dies of the darkspawn taint if Duncan is not present to save the PC by making them a Warden.
The Dwarven Noble, without the Wardens to chance upon, would have eventually died in the Deep Roads after being exiled.
The Mage PC is the only (more-or-less) character with a chance of surviving the events of his or her origin without Duncan's assistance (by collaborating with First Enchanter Irving)—only to most likely fall prey to the event that troubles the Circle after Ostagar.
Nails eventually decide which of the three routes you take in the opening of Fate/stay night. The best example is probably the choice leading to "Unlimited Blade Works": If Shirou recalls Saber before she slashes Archer, Archer is left unwounded and capable of participating in the Grail War at full strength. This in turn boosts Rin's position in the war, making her a competitor to Shirou instead of someone forced to rely on him as an ally (and also makes Ilya not notice Shirou). Thus, "Fate" and "Heaven's Feel" get locked out because everything begins snowballing from that decision and Archer now being in an ideal position to put his true agenda in motion. The difference between "Fate" and "Heaven's Feel", meanwhile, is decided by several nails during the opening that decide if Sakura's mental barriers are maintained or fall because Shirou is paying attention to her, making her open to manipulation from Zouken.
The Playstation Portable version of Persona 3 hints at what would happen differently if the gloomy looking main character were replaced with an energetic looking girl. The answer? Not very much, it seems. She still sacrifices herself to hold Nyx back. The very most she can do is prevent the death of Shinjiro Aragaki. And he only lives a few more months, since he's dead in the canonical "The Answer".
Except Persona 3Portable came out after FES, so it's possible Shinjiro is still alive in the Female PC's version of The Answer.
Resident Evil 2 begins this way for the main characters: whichever end of the car Leon wrecks into the pole determines which events Leon and Claire will experience respectively and how they transpire (including which one of them encounters the Tyrant).
Mobile Suit Gundam: Gundam vs Zeta Gundam has several What If? storylines, but the one that best fits this trope is the Project Zeta story, where Garma Zabi surviving his fate from the original series, which leads to other characters killed by Amuro and the Gundam surviving, and eventually to Zeon winning the One Year War. But then it veers sharply into In Spite of a Nail, as the rest of the storyline is just First Gundam's events played out with older characters and Zeta Gundam-era mecha, even when several of those events already occurred even in the altered timeline.
There are a couple of other noteworthy alternate story paths; each of the three big heroes (Kamille, Amuro, and Char) has a storyline where they end up with the Titans, with varying degrees of believability note For Kamille, the AEUG caused the deaths of his parents so he wants revenge; Amuro and Lalah (who is still alive here) joined the Newtype labs, which were later absorbed by the Titans; Char's plot ties into Project Zeta, as he joins the Titans as Quattro Bajeena after he kills Garma. There's also a route that re-creates Char's Counterattack six years early and is a Kill 'em AllDowner Ending.
In the Fire Emblem Jugdral timeline, the Big Bad has a Quirky Miniboss Squad named the Dark Warlords. Well, in the second game of said saga (Thracia 776), some of the Warlords are people from your own chara roster, who end up on the enemy side under different circumstances: getting killed in battle, not being recruited, or not being saved when they catch the Distress Ball. These charas are: Tanya's father Dagdar, Mareeta's father Galzus, the thief Lifis, Manfloy's granddaughter Sara, and Team Mom Evayle.
In Throne of Bhaal, the Solar reveals that Sarevok, the first Big Bad of the series, was also one of the Bhaalspawn children about to be sacrificed at the temple where Gorion found and rescued you. Gorion only had the opportunity to save one child, and he chose you instead of Sarevok. The Solar then shows you a vision where Sarevok was saved and you were not: he wasThe Hero, and you were an evilerBig Badthan he ever was.
In Mortal Kombat 3, Sub-Zero escapes from the Lin Kuei, and his friend Smoke is turned into a cybernetic ninja in his stead. However, Mortal Kombat 9 starts when the future Raiden (following the conclusion of Mortal Kombat Armageddon) sends a message to his past self warning him about the apocalypse that will occur. One of the changes that occurs as a result of Raiden's tampering with the past is that Sub-Zero becomes a cyborg instead of Smoke.
Also, one of the visions Raiden received was of Liu Kang dying and being turned into a zombie (the events of Mortal Kombat Deadly Alliance). In an attempt to avert Liu Kang's death, Raiden has Kung Lao fight Shao Kahn in Liu Kang's place during the Outworld Mortal Kombat tournament. It didn't work: Kung Lao died by Shao Kahn's hand, and Liu Kang would later die anyway...by Raiden's hand.
Additionally, Raiden's slaying of Motaro in the reboot causes Shao Kahn to sacrifice Shang Tsung (one of the series' recurring villains) to power up Sindel (who in the prior timeline, made a Heel-Face Turn). Using this power, she easily kills a majority of the heroes, finally requiring a heroic sacrifice by Nightwolf to kill her.
Metaphorically speaking, the Big Bad of Radiant Historia spends much of his time pulling out nails—there's only one possible timeline that doesn't contain The End of the World as We Know It, and surprisingly small changes can prevent that timeline from coming to be. The main character, in turn, has the obligation to find the nails and hammer them back in. One easy to follow example is a soldier whose sword breaks in battle, causing him to get killed. If you get him a replacement sword, he survives the battle and saves the lives of some of his comrades in the process, and they will be able to serve a critical role in a later battle.
To give you an idea of the scope of this, one of the first things Stocke does is tweak a nail himself to create two completely distinct timelines. Often, nails in the "True history" are so bent he needs to go to the "alternate history" to find replacements and bring them back, despite his goal being to ensure the alternate history never has to occur in the first place. The only reason the timestream doesn't collapse like an accordion is his method of time travel explicitly comes with an infinite-use Get Out Of Causality Free card.
The rope in Cave Story. It's the single most important key to stop the destruction of everything in the island, including a large percentage of the cast and get the happy ending. And it's incredibly easy to miss. If you don't get it, expect some rough times in the plot.
Front Mission 3 is like this. There are two story arcs with vastly different events (although they lead to mostly the same conclusion) and which one you take depends entirely on a mundane choice in the beginning of the game to go with your partner to do a drop off. If you stay, you see an email from your sister saying shes in town at a military base, which you coincidentally happen to be at later when a massive explosion goes off. You then attempt to look for her right then and there. If you went with your partner, you don't have time to check your email before the explosion, so you leave the site without realizing your sister was there until later, requiring you to use a different method to get in and meeting different people from different (and opposing) factions.
In Starcraft II, there is a Bad Future prophesied if Sarah Kerrigan is killed. In the "Wings Of Liberty" ending cinematic, Jim Raynor basically prevents it from happening by moving his shoulder a few inches to the left, taking a bullet meant for her by Tychus (and since Raynor was wearing armor, there was no serious injury).
Zeratul, apparently aware of this trope, appears in both Wings of Liberty and Heart of the Swarm to hand the main character some emergency nails, first by giving Raynor the Ihan Crystal and thus another cause to save Kerrigan besides his love, then by directing the Swarm to Zerus, so that Kerrigan is cleansed of any remaining influence Amon might still have by becoming Primal Zerg. The latter becomes doubly a world-saving nail, since without the tag-along Dehaka, who was immune to the Psi Disruptor, the entire Swarm would have been killed over Korhal.
Discussed and shown in Injustice: Gods Among Us. The Regime universe was a world where Superman took it over after the Joker causes him to kill Lois and destroy Metropolis. In the main universe, the Joker did get the nuke to blow up Metropolis, but never got to use it as he was dragged into the Regime universe with a number of others.
Half the fun of Dwarf Fortress is caused by this sort of thing. A stray cat distracts a cyclops, causing it to avoid your traps. A dead butterfly props open the door, letting goblin ambushers in. A mechanism in a magma floodgate was made from orthoclase, causing the floodgate to fall apart and melt while the magma pours unchecked into the fortress...
This is the "Hypothetical path" story mechanic of Dynasty Warriors 8 in a nutshell. Unlocking each faction's happier outcome involves changing historical events during enough battles to stir up a knock-on effect that changes a crucial moment (such as Guan Yu's death at Fan Castle) and completely redirects history.
The Star Trek Online mission "Temporal Ambassador" is a continuation of TNG: "Yesterday's Enterprise". Because Natasha Yar and the Enterprise-C ended up going forward in time after the episode instead of backwards, the player winds up in a timeline where the Klingons conquered the Federation, then were too weak to fight off the Dominion.
Super Robot Wars Original Generation explores this in a limited extent with the Shadow Mirror universe. In the regular timeline, Kyosuke Nambu and Excellen Browning were involved in a space shuttle accident; Kyosuke survived due to his incredible luck, while Excellen technically died and was brought back to life by plant-like aliens called the Einst who were looking for an "Eve". In the Shadow Mirror universe, the Einst chose Kyosuke instead, which resulted in his becoming the Ax-Crazy Beowulf (who's upgraded to Big Bad in the anime adaptation, The Inspector). Without the Einst resurrecting her, Excellen's family instead had her body "revived" her as a cyborg who took on the name Lemon Browning and ended up joining Shadow Mirror. For cosmic irony points, the mainline Kyosuke and Excellen are a couple, while Lemon's lover is Axel Almer, Beowulf's arch-nemesis.