Star Trek: The Animated Series, "Yesteryear", in which Spock and Kirk find themselves in an alternate timeline where a young Spock died and an Andorian is in Spock's place. As it turns out, Spock's Set Right What Once Went Wrong by posing as his older cousin is part of a Stable Time Loop and the alternate timeline was because he took too long with his earlier trip through the Guardian of Forever.
The entire series would not have happened if A) Fry hadn't run into Bender at the suicide booth, B) They didn't run into Leela at the diner, C) If it wasn't Tuesday when Fry and Bender went to the head museum, D) If Bender hadn't broken a lightbulb on his antenna, changing his programing, and E) If the professor didn't have his previous crew's career chips with him on the ship. This is subverted with Fry falling into the tube in the beginning because it is later revealed thar Nibbler knocked him in to help save the world in the future.
"The Farnsworth Parabox," which features a universe "exactly like ours" except for the fact that the results of all coin tosses (or at least those in the recent past) are reversed. (According to the DVD commentary, it's a probability maths injoke.) This leads to results like Bender being gold-plated, and Fry and Leela being married. Oh, also the colors are all mixed up, the sky is bright and swirly and the background music is a Theremin. How'd we forget that? Other perpendicular universes (parallel universes, like the cowboy universe, never intersect) are visited, including a universe where everyone lack eyes, where their heads are bobble-heads, where everybody is a robot, a Roman Empire-themed universe (complete with Roman numerals calculus) and a hippie universe... however there do seem to be universes without the main characters, such as an octopus universe, a universe filled only with women and a completely frozen universe.
In "All the President's Heads", the gang travels back in time to The American Revolution to stop Prof. Farnsworth's ancestor David, who betrayed the Revolutionaries by counterfeiting money. After they stop David, Fry burns the counterfeit bills with a lantern he found in a church, which turned out to be one of the lamps used to signal the coming of the British (one if by land, two if by sea). Because of this, the British win the war and the gang come back to an America that's still under British rule.
In "The Devil's Hands Are Idle Playthings", Robot Devil sets up a "ridiculously circuitous plan" that bounces from Bender, Calculon, Leela, and Fry's opera which ends with either him marrying Leela or getting his robot hands back from Fry.
Most of Timmy's time traveling adventures in backfire because he doesn't realize until it's too late that he was the nail that made things go wrong; for instance, a Stable Time Loop involving Mr. Crocker's obsession with fairies.
Not to mention the episode where he wishes he was never born. Tuns out his gender is a nail as well - his parents had a girl instead, and the life of everyone Timmy knows is better for it.
There was also the episode "Father Time" where Timmy, after melting his dad's trophy with Heat Vision, goes with Cosmo's crazy idea to go back and time to stop his father from winning the stupid trophy in the first place. When that happened, Timmy's dad gets the last place prize; an all expense paid scholarship to Dictator School, where he rules Dimmsdale in a dark future with creepy happiness and never got to marry Timmy's mom. So Timmy doesn't exist and lost his godparents (who vanish JUST before the revelation of Dictator School).
In the Totally Spies! episode "Futureshock," the spies' rival, Mandy, breaks a nail during a cheerleading practice (the incident possibly being a Double Entendre) and being the vain, shallow type she is, believes this makes her flawed. After David suggests she take up student broadcoasting until her fingernail grows back (since no one will see her hands while she's at a newsdesk), Mandy does so and develops a liking for it. After the spies are accidentally sent into the future (where Mandy now rules Beverly Hills and has renamed it "Mandy Hills"), they discover that Mandy (now with her own TV-network and numerous TV-shows about herself) went from having just one talk show at Beverly Hills High School to running "Mandy Media Enterprises" all in the span of just a month—they also discover that Mandy plans to Take Over the World by "Mandifying" the entire planet. Fortunately, the heroines (teaming up with their future selves) manage to defeat her, and after being sent back to their original time period, they get some WOOHP-issue nail polish to stash in Mandy's locker, which (after putting it on her nails) makes her nails regrow and she decides to go back to cheerleading.
On the fifth season finale of Family Guy, Peter goes back in time to sow his wild oats and ends up not marrying Lois, who married Quagmire instead. Apparently, their not marrying allowed Al Gore to become President — and Gore apparently killed Bin Laden, instituted zero-tolerance gun control and universal health care, and fixed the public school system. In addition to all that, Dick Cheney shot Tucker Carlson, Antonin Scalia, and Karl Rove. With one bullet. Brian likes it this way. Whew. Even after they "fix" the time-stream, the present still isn't the same: somehow, Roger the Alien ended up in their house.
Done in a Christmas episode of American Dad!. Stan was sent back to 1970 to renew his Christmas spirit, and uses the opportunity to kill Jane Fonda, whom he blames for modern day liberalism. Though instead of killing her, Stan somehow convinces Martin Scorsese to quit drugs and thus Taxi Driver was never made; as a result, John Hinkley, Jr. never got obsessed with Jodie Foster, and never tried to assassinate Ronald Reagan to impress her. Reagan loses the election to Mondale, who immediately handed America over to the Soviets. The timeline is fixed by the end of the episode (Stan shoots President Reagan), except for Roger who became the inventor of disco, because he found a Best of Disco cassette that Stan accidentally dropped in 1970. And guns are easy to get because Stan neglected to shoot Brady, thus no Brady Bill.
Subverted in the Fantastic Four: World's Greatest Heroes 2007 animated series episode "Out of Time". While the Four are on a field trip to prehistoric Earth the Thing swats a mosquito, just as Mr Fantastic warns them not to change anything. The camera then pulls back to show he's already killed a dinosaur. Reed later assures him that this can't possibly have had the effect of Dr Doom ruling the world. But when the Torch gives cavemen the secret of fire, he's worshiped as a god in modern New York (although In Spite of a Nail, 15,000 years of Johnny Storm worship hasn't changed anything except the Statue of Liberty).
Justice League, "A Better World" has an alternate universe where the League is a group of "well-intentioned" extremists, set off by the nail being the death of their Flash. Implications of this episode would face the main continuity for nearly the remainder of the show.
Ben 10: Alien Force: In "Time Heals", Gwen goes back in time and stops Ben and Kevin from tampering with the Omnitrix and causing the current mutation that Kevin is suffering and Wangsting over. Apparently, Kevin's mutation provided the key to victory in a future battle with Hex and Charmcaster, as they have taken over the city when Gwen gets back to her own time.
Beast Wars: G1 Megatron wanted to have any descendent with the possibility try this (he somehow knew he wouldn't be alive to try it himself by the time the technology that'd allow time travel would be developed enough for this), with the nail being killing G1 Optimus Prime as the original transformers slept on prehistoric Earth, in order to sway The Great War into the Decepticons' favor because of course Optimus never dies, and when he doesit's always permanent. Beast Wars Megs very reluctantly tried this once, because he likely knew had he no other options, Unicron would've likely killed everything in this time continuity. When the timeline is restored by the Maximals and the Heel–Face Turn Blackarachnia, Megatron decides to try something a little different and goes after the primitive humans, as their help would later assure Autobot victory over the Decepticons.
Freakazoid! inverts this. The titular hero ends up at Pearl Harbor in December 1941 and stops the Japanese from invading. When he comes back to the present, the world seems to be a better place: Sharon Stone can act, Rush Limbaugh's a "bleeding-heart liberal", EuroDisney is booming, cold fusion works, and there are no Chevy Chase movies. Just one catch: the Brain is President.
Inverted by having Homer's guardian angel Werner Klemperer show Homer what his life would have been like had he not married Marge. In the alternate timeline, Homer is rich and happily married to a beautiful woman, while Marge is the President, enjoying both success and popularity. Needless to say, this was not a successful trip for the guardian angel.
In a "Treehouse of Horror" sketch, the Butterfly Effect is taken to ridiculous extremes as Homer keeps traveling back in time and each time he steps on something, it changes the future in wildly differing ways. He comes to a future where the family is wealthy, his sisters-in-law are dead... but no one has heard of donuts. Homer runs back in time screaming (meanwhile it is raining donuts outside) and just indiscriminately squashes whatever is around him. He comes back to find everything normal... except everyone has forked, lizard-like tongues. He shrugs: "Close enough."
In the Phineas and Ferb epsiode "Phineas and Ferb's Quantum Boogaloo", future Candace travels back in time and helps her younger self bust Phineas and Ferb on the first day of summer. When she returns to her own time, she discovers this act has lead to the tri-state area becoming a dystopia ruled by Doofenshmirtz. She then has to travel back in time again and stop herself from helping her younger self from busting her brothers.
A sketch shows what would happen if jerks got a time machine. It ends with one jerk stopping Nazism from ever getting started by humiliating Hitler, thus becoming a Hero with a Time Machine.
In a parody of Popeye, an angel shows Wimpy what would have happened if he did not exist when Wimpy attempts suicide. Popeye and Brutus are friends, Olive has huge breasts, Goon gains a doctorate, there is no war, and all hamburgers are free. The angel, seeing that he failed, pushes Wimpy off the bridge.
In a parody of If You Give a Mouse a Cookie, the mouse tries to wash down the cookie with the boy's mother's breast milk, but accidentally drinks her blood instead, turning him into a vampire, who makes various people his followers, on whom the US government declares a nuclear war, which other countries get involved in, destroying the whole world. The ending reveals this as a story the mother tells the boy, to explain why she killed her husband for "giving a mouse a cookie".
Similar to the Popeye example, there was a Christmas Episode of Beavis and Butt-Head where an angel shows Butt-Head how life would be without him, showing things like Principal McVicker being normal and Beavis working at a soup kitchen with Stewart. Despite this, Butt-Head's influence still permeates into this universe, too.
The Legend of Tarzan: Jane plants a little flowering vine because she can't stand how ripe fruit smells. The vine grows and starves out all the food the Elephants need. So the Elephants move into the Gorilla's territory until the vine is gotten rid of. Fifteen minutes later, the Elephants and Gorillas are trying to kill each other.
In the Rated A for Awesome episode "Thera's Date With Destiny" Noam's new future-predicting invention shows that Thera will be going to prom with Chet. They try to change the outcome, but each attempt either has them start dating even sooner or she goes to prom with someone else she doesn't want to go with. That is until the last vision, which doesn't show her date's face, but it's hinted to be Noam. Each vision after the first also shows her with a different hairstyle.
Ultimate Book of Spells: When the Wizarding School went into a field trip to the past, Gus took a crystal as a souvenir. Unfortunately, without that crystal to power up his wand, Cassy's great-grandfather couldn't defeat Zarlak, resulting in a Bad Future where Zarlak rules. Fortunately UBOS managed to take the heroes back to the past to set things right.
The Where on Earth Is Carmen Sandiego? episode "Timing is Everything" had one of Carmen's henchmen, Mason-Dixon, go back in time and tamper with one of Carmen's first heists. After he caused her to fail at evading the police, she went on to become his discouraged henchwoman.
In the fifth season premiere of Adventure Time, Finn wishes that the Lich never existed, creating an Alternate Timeline where the Lich never came to be. Things go downhill from there very rapidly. And to top it off, the Lich is born anyway, although several years later than he would have and in a radically different form.
In the Lilo & Stitch: The Series episode "Melty", Lilo embarrasses herself in front of her crush Keoni and goes back in time to make it so it didn't happen, but her every attempt to stop it from happening makes everything far worse. In the end she fixes everything by going back and recreating the embarrassing moment.
An episode of Jacob Two-Two had Jacob accidentally break his older brother's Beatles record and use a time machine from his spy neighbor (seriously) to go back and fix it, but Jacob messed up something else that he had to go back and fix, etc. Ultimately, he was able to fix everything except his brother's record from being destroyed, but it turned out his neighbor had a copy anyway.
The Looney Tunes Show: In "Best Friends Redux", Daffy travels back in time to prevent Bugs from meeting his childhood best friend Rodney Rabbit. In doing so, he creates a present where Bugs never met him and no one knows who he is.
In the Danny Phantom episode "Masters of All Time", Danny goes back in time to stop Jack from accidentally turning Vlad half-ghost. The result is that Jack ends up half-ghost, and Vlad and Maddie are married and living rich lives in Wisconsin. It is more or less subverted in terms of personality: Vlad is still manipulative and controlling, lying to Maddie so she would leave Jack, Maddie is still very obsessed with ghosts and in love with Jack, and Jack is still in love with her, and more or less a decent guy who unlike Vlad, did not abuse his powers for personal gain.
Parodied in one of the Cold Opens of Arthur. The Brain builds a time machine at school so that the gang can explore the time of the dinosaurs, and warns his friends to stay within marked boundaries in order to avoid messing up time. Unfortunately, Buster just happens to be eating a box of raisins as they went exploring, and the box accidentally falls from his pocket, off the path, and outside the boundaries. It isn't until everyone returns to the school that they realize that they now have scaly, lizard-like limbs, all thanks to that one box. Mr. Ratburn invites them in to class, also having lizard-like legs, and eats a fly as the intro comes to a close.
In Alvin and the Chipmunks, Alvin wins a sweepstakes where he's offered one of two prizes: $500 or a mystery prize that could range anywhere from a free lunch to millions of dollars. He's shown two alternate futures. In the first one where he takes the $500, he ended up investing it and continuing his singing career, and as a result, he and Brittany are filthy rich, Simon and Jeanette are successful scientists and Theodore and Eleanore run a booming restaurant business. In the future where he takes the mystery prize, he just gets a free lunch which gives who food poisoning, weakening his vocal chords and forcing him to give up singing, which causes him and everyone else to be poor. Ultimately, it was subverted, because when Alvin calls to claim the $500, they realize he's only a kid and explain to him that he had to be at least 18 to enter the sweepstakes.
Looped is about two friends stuck in a "Groundhog Day" Loop and every episode takes place on the same Monday, but the day keeps going differently depending on their actions.
ˇMucha Lucha!: In "Woulda, Coulda, Hasbeena", Señor Hasbeena goes back in time to prevent himself from losing a crucial fight and the three mascaritas go after him to protect the timeline. While in the past, Buena Girl collides with the Headmistress' past self. When they return to the present time, the classroom is full of Buena Girls asking if the story will be on the test.
In the Direct-to-Video, Our Friend Martin, a teenaged African American boy, his white best friend, and two other kids, another white boy and a Latina girl, go back in time to save a teenaged Martin Luther King Jr. after learning that he was assassinated. When they come back to the present, the Civil Rights Movement never happened and as a result, the protagonist's "best friend" angrily tells him he doesn't talk to "negroes," Jim Crow laws are still in effect, the Latina girl works as a cleaning girl alongside her mother and doesn't speak English, the feminist principal now teaches home-ec., and doesn't respond to the principal's sexist insult. When he goes home, he learns that his mother, a self employed business woman, works as maid. Things only go back to normal when King decides to back in time, and accept his role in history.