Adventures in Zambezia has Zoe whose biological parents are never seen, but it's implied that they were killed by Budzo, leaving her in the care of Sekhuru.
Aladdin: The title lead is an orphan and homeless, and Princess Jasmine's mother is dead. We see Al's parents in one comic, and meet his dad in King of Thieves. Aladdin had a mother in early drafts, and Aladdin even sung a song called "Proud of Your Boy" about trying to make her proud, but the idea was ultimately scrapped, and Aladdin mentions in King of Thieves that she died when he was a kid.
Atlantis: The Lost Empire: Milo's parents, according to disc 2 of the two-disc DVD of the film, were both killed in a railway accident when he was still a baby, and was raised by his grandfather, who was Preston Whitmore's best friend, who apparently died much later (and according to Whitmore, as a broken man); while Kida's mother the Queen was killed trying to save the titular Atlantis from the tidal wave which then submerges her kingdom, and her father King Nedakh is killed by internal bleeding thanks to an injury he received from Rourke as an attempt to steal the Crystal and kidnap the princess, and in the case of the latter, it also caused her to become a Queen herself at the end of the film.
Bambi: The eponymous character's mother is shot by a hunter. His father, who is distant and mysterious, subsequently begins to take care of Bambi. (This somewhat matches the life-cycle of real deer and was part of the original book.)
Don Bluth is similarly in love with this trope. Fievel spends An American Tail trying to locate his parents, and there is a deeply depressing scene with some orphans in an alley toward the end.
Edmond from Rock-A-Doodle also has both parents but they only appear in the live-action segments in the beginning and end. He asks where they are a couple of times during the animated section but never gets a response. (They're fine though.)
In The Land Before Time, Littlefoot has no apparent father, although one of the later movies introduces him. His mother, however, passes away less than halfway into the film. Cera has a father, but her mother disapears early on. Petrie only has his mother, and except in the original movie, neither does Ducky.
Spike, however, is a true case of this trope, seeing as he was apparently abandoned as an egg.
Their T. rex friend Chomper actually does have both parents, though he is separated from them for awhile at the beginning of his life due in part by Littlefoot and his friends (they were attempting to rescue an egg that the egg-eaters were trying to eat, but a mixup caused by a landslide resulted in Littlefoot and his friends unknowingly bringing a Sharptooth egg into the Great Valley).
Anastasia (or Anya) is raised in an orphanage until she's 18 years old. Here, the Parental Abandonment is fairly central to the plot and feels a lot less tacked on than usual.
And certainly, it's worth bringing up Titan A.E. in this context: the destruction of Earth effectively orphans her handful of surviving species. Humans are explicitly described as an "orphaned race". The main character is also an orphan; his mission is not only to find the Titan, but to find his father, whom he finds out about halfway through the film is dead.
Cinderella, like Snow White and as per the classic fairy-tale, is at the mercy of a wicked stepmother. Her biological mother died before the film begins and her father dies during the prologue.
The prince's mother is presumably deceased. His father is around, but it's indicated that there's some distance between them. (The king seems to think his son is a rebellious boy who just needs to settle down and produce some heirs already.)
Aladar from Dinosaur gets separated from his parents while he's still in his egg, and then gets taken in by a family of lemurs. They likely died in the meteor shower years later, if not sooner.
Kuzco in The Emperor's New Groove is a spoiled eighteen-year-old Emperor with no parents anywhere in sight. The only mention of this comes in this exchange between Kuzco's incredibly ancient (and recently fired) adviser Yzma and her lackey Kronk:
Yzma: Who does that ungrateful little worm think he is? Does he... have any idea of who he's dealing with? How could he do this to me? Why, I practically raised him! Kronk: Yeah, you'd think he would have turned out better. Yzma: Yeah, go figure...
Well, If Yzma's statement and implied personality meant anything, it seems we know why Kuzco was a jerk.
Played with in The Fox and the Hound. A hunter kills a fox cub's mother at the very begining, making a woman adopt him. However it's not for long because she has to abandon him on a wildlife reserve to save his life.
Frozen: Anna and Elsa's parents die in a shipwreck early on, leaving them orphans by the time the film's main events happen. There is also no mention of what happened to Kristoff's human parents.
How to Train Your Dragon 2 reveals that Hiccup's Missing Mom Valka is not dead like assumed (though being carried off by a dragon made it a very good assumption), and she'd been living in the wild with dragons for the past twenty years. It was entirely possible for her to return to Berk, but she had developed a "dragons are better than people" mentality and refused to go back to a place that would fight them.
Both played straight and inverted. Manfred is an abandoned parent - (his family was killed by hunters); Sid's family abandoned him because he was annoying; Diego abandoned his pack; the human baby was simply "misplaced". His mom is killed by a smilodon, and he is reunited with his dad at the end.
2: Ellie was separated from her herd, and her adopted opossum mother is presumed to be deceased.
In Jack and the Cuckoo-Clock Heart, Jack's birth mother decides that the midwife Madeleine would be able to take better care of Jack than she ever could, so she leaves the night after she gives birth to him. There is no mention of his father at any point in the film.
Mowgli's birth-parents are deceased. On top of this, the wolves that raised him appear very little. They were quite major in The Jungle Book book, according to which his biological parents were killed by the tiger Shere Khan.
The final scene reveals his birth father is alive in a hidden panda village.
In Lilo & Stitch, Lilo is raised by her sister Nani after their parents were killed in a car accident. Stitch is also somewhat traumatized when he learns that he has no conventional family, as he was artificially created in a lab. The Mad Scientist responsible eventually becomes a father figure, though.
In Moana, Maui's situation is a doozy. He was born human. He was tossed in the ocean shortly after birth and left to die, only surviving (and eventually gaining demigod status) because he was 'chosen' by the ocean.
The Princess and the Frog: While Naveen's parents are alive, they refuse to financially support him because of his partying and womanizing, so he's functionally this.
Played for Laughs in Ralph Breaks the Internet. When Vanellope is interrogated by the other Disney Princesses, Princess Jasmine asks if she has daddy issues. When Vanellope mentions that she doesn't even have a mom, many of the aforementioned princesses above cheerfully exclaim "Neither do we!"
In the first The Rescuers movie, Penny (the child in distress) was explicitly an orphan (though it gets better for her in the end); in the second, Cody's dad was "gone", and his mother's voice was heard twice, from offscreen. (As a matter of fact, a few fans have theorized that Cody is adopted by Marahute, the golden eagle he saves, as she's a far more interesting mother figure in the boy's life.)
In Rise of the Guardians, Jack's creator, the Man in the Moon, simply made him into the spirit of winter and gave him his name before leaving him to his own devices for centuries. Jack is shown trying to get his attention by speaking to the full moon, and it's entirely possible that Manny can hear him, but he never responds. Obviously, this doesn't help Jack's development, especially when Manny suddenly decides that he needs him to join the Guardians of Childhood.
Shrek's parents were written out of the script (originally he wanted to become a knight and they disapproved). According to the musical, his parents threw him out and, in Shrek The Third, his father tried eat him.
Fiona's parents placed her in a lonely tower "for her own good"
Arthur's parents are presumed dead if he's Fiona's only other relative. As we find out later in Shrek the Third, his father abandoned him, through we don't know what happened to his mother.
Donkey is sold by his "grandmotherly" owner and we never find out what happened to his parents.
Snow White: The titular girl was raised by a wicked stepmother. Some versions of the fairy-tale have her father still alive, but in the Disney film he's nowhere in sight.
Surf's Up: Cody and Chicken Joe's fathers were eaten by a whale and fried for dinner, respectively, and Lani was apparently raised by her uncle, the Geek/ Big Z.
In The Swan Princess, Prince Derek has a mother but no father, and Princess Odette has a father but no mother. This is a particularly mind-boggling example, as Odette has just been born at the start of the movie, but there's not even a single mention of her mother — just "happily, a daughter was born," as if the stork paid an unexpected housecall.
It's probably safe to assume that she died in childbirth. But then it's odd that the moment is entirely treated as the happiest of days, when it reality there would also be sorrow over the death of the queen. Of course, death by childbirth isn't always immediate she could have died a few days or weeks later.
And then later in the movie, Odette's dad is killed, leaving the poor girl with no parents.
Inverted in Tangled where Rapunzel was kidnapped as a baby and raised by Gothel, thinking that she was her mother. Her real parents never gave up hope trying to find their missing daughter and they were happily reunited with her at the end of the movie. However, it was played straight with Flynn/Eugene, who is an orphan.
Tarzan is an orphan; his parents were killed by a leopard.
He gets a loving mom in Kala. Though his adoptive dad Kerchak doesn't accept Tarzan as his son until he (Kerchak) is on his death bed.
Films — Live-Action
In Angel, both of Molly's parents abandoned her. Her father disappeared when she was 6, and her mother ran away to New York with her new boyfriend when Molly was 12; leaving behind a note and $100. From the way Molly talks about him, Lt. Andrews initially assumes her father is dead, and it is only when she says she is waiting for him to come back that he realizes that the father also abandoned her.
Angel and the Badman: Quirt Evans was adopted and named by a rancher named Walt Ennis after his birth parents were killed in an Indian attack. Ennis himself was later murdered.
How Annie ended up a foster kid. And the other foster kids as well.
Are We There Yet?: Lindsay and Kevin think their divorced father is going to come back any day now and try to reconcile with their mother, so they scare away all her dates while waiting for his return. Then they find out not only has their father been lying to get out of spending time with them, hes remarried and had a new baby without them even knowing.
Delayed version: In Away We Go the lead characters are forced to find another place to live when the man's "heroically self-absorbed" parents leave the country and rent their (the parents') house to strangers. Apparently their son's girlfriend being pregnant and effectively homeless wasn't a good enough reason to delay a refreshing move.
A Bad Moms Christmas: Apparently, Carla hadn't seen Isis for years by the time this movie rolls around and, after Carla lends her money, she disappears yet again. From what Carla says, she's had a history of just vanishing. Her father meanwhile is not mentioned once.
The version of The Penguin in Batman Returns suffers this trope in the worst way possible. Born horribly disfigured, his parents, the rich and ritzy Cobblepots saw him as a shame to their family. As such, they took him to the park and actually threw his stroller into the river which took him into the sewer where he was found and raised by the zoo penguins. It's no wonder he hated surface-dwellers and attempted to destroy Gotham.
Belle: Dido's mother dies of unknown causes in her childhood. Then her father, who she'd never seen before, delivers Dido to his family in England. He never appears again; she is raised solely by them.
In Blade Runner, Rachel is a Replicant: a biological android without parents who has false memories of having a family implanted to give her emotional stability.
Another one of Ridley Scott's works, Prometheus, has this as its Central Theme. The "Engineers" left the human race to fend for itself, and then attempts to exterminate it. Peter Weyland built the most powerful corporation on Earth, and his daughter Vickers worked hard to be worthy of inheriting it, only for Weyland to seek immortality via the Engineers instead. Shaw discovers that she's pregnant with an alien fetus, and immediately has the autodoc cut it out of her and attempts to kill it.
Shaw: Why do you hate us?
Well, the "Engineers" are genetically identical to humans, and humanity's answer to that question seems to be Because you're not what we wanted.
Invoked by David. "Don't we all wish for our parents to be dead?" Weyland programs him, serving as sort of adoptive father, and without him, David would consider himself to be free.
One particularly loathsome father in Blossoms in the Dust drops off his newborn son at Edna's orphanage (the mother died in childbirth) because he just doesn't want to be bothered with taking care of the baby. When said father finds out the baby was adopted by a rich family, he comes back, looking for a payoff.
Patrick "Kitten" Braden from Breakfast on Pluto is the product of an illicit affair between the local Catholic Priest and his beautiful young housekeeper. As such, he is promptly given up for adoption and raised by an uncaring foster mother. The film revolves around Patrick's search for the mother who abandoned him.
Breaking the Girls: Sara's father abandoned her as a child. Then her mother died, so she lived with her aunt.
In Cinderella (2015), Ella's mother dies while her daughter is a young girl. Her father later leaves for a long trip, and dies shortly after.
Closet Land: The Author's mother is dead, and her father simply isn't mentioned at all but he appears to have been absent from her life for whatever reason at a very early age.
Cher in Clueless is a half orphan; her mom died due to a freak accident during a routine liposuction, although she still likes to pretend she's watching over her. Josh even ribs her about her desire to makeover Tai being a manifestation of her having no mother and treating her as a Barbie doll. Later (in one of the few played straight scenes), when she is insecure that she isn't enough of a 'do-gooder', her father tells her that he hasn't seen such good-doing since her mother.
Subverted with Josh, however; despite having divorced his mother and having no blood-relation to Josh, Cher's father makes a point of being a devoted father figure to him. ("You divorce wives, not children.")
Contact: Ellie's mother isn't shown or mentioned. Her father died of a heart attack in her childhood.
Likewise, the French film La Fracture du Myocarde (known in English-speaking countries as Cross My Heart) deals with a boy's attempts to keep the authorities from learning that his mother has died and he's living on his own.
All 3 main characters in Darkness Falls. The lead's mother was killed by the Tooth Fairy when he was ten, and since he became a ward of the state, Parental Abandonment must apply to his father too. Then later the other little kid is in the hospital, and his twenty-two-year-old sister Emma Caulfield is making the medical decisions. The parents are simply never mentioned, although under the circumstances they're probably dead.
In Doomsday, Eden's mother managed to get an army helicopter to take her out of a plague-infected Scotland when she was four years old. She had an envelope with her mother's address, so she would know where to go when she's older. A grown up Eden does eventually get to go to that address, and her mother's dead. The Disappeared Dad is never mentioned.
Empire Records: Lucas' mother turned him over to the state when he was twelve "for being a bad seed", Berko appears to be living alone in a cabin behind the store, Gina, AJ, Eddie and Mark's parents are never mentioned, nor is Corey's mother, and when Deb is asked about her mother, she says something along the lines of "If you find her, let me know — I'd like to talk to her too".
The Final Girls: Max's father is not around it seems as he's never seen or mentioned. Whether he died, was just never involved or what is not explained. Amanda dies in a car accident early on, which Max also has a hard time dealing with. It's especially tough going to one of her movies on the anniversary. Then, once Max is sucked into that movie, she meets the character her mother played come to life. This is also clearly painful for Max. Then the character is killed while saving Max, which is like losing her all over again.
In Georgy Girl the protagonist deals with her roommate'sShotgun Wedding to a handsome rake, roommate's pregnancy, all before the roommate leaves her husband, Georgy, and the baby for a wealthy man; By the time the rake (who was Georgy's lover for a while) leaves them, Georgy has been caring for their baby like she was her own.
In Godzilla (2014), it's implied that Joe Brody was less than a stellar parent after his wife's death. He's still in relatively good terms with his son despite this.
Gone: Jill and Molly's parents are both dead. The trauma of their loss resulted in Jill having attempted or at least being viewed as a risk for suicide, which meant she spent a bit of time in a mental institution.
Happiest Season: Abby lost both her parents when she was 19. She plays up being an orphan while visiting Harper's family cheerfully, but later quietly cries over her loss, which still affects her.
Hawk the Slayer: Voltan kills his and Hawk's father. Their mother is not mentioned.
The Japanese film The Homeless Student delivers a one-two punch: first the mother dies, then the children come home from school to find all their belongings outside the apartment. The shiftless, frigid father rides up on his bicycle to explain he has gambled away all the family's money and hasn't paid the rent. Then he rides off again, leaving his three children to fend for themselves. What.
In The Hunger Games teenage girl Katniss has to take care of the family because her mother fell into a severe depression after the father died. Later, a second stroke of fate forces the mother to assume motherly obligations.
Dom's children in Inception. Their mother, Mal, is dead, and Dom has been framed for her death and can't enter the U.S. or any country that has an extradition treaty with it. He agrees to get involved in the film's plot because it will let him see his kids again.
Ingrid Goes West: Ingrid's mother died of a heart attack a few months before the movie started. Ingrid describes her mother as her best friend and gradually admits that she doesn't know how to cope without her. Conversely, her father is never seen or mentioned.
Nell and Eva's dad dies early on due to an accident with the chainsaw.
Nell and Eva's mother apparently died sometime prior to the events of the film. She's only seen in home videos from years before (though the last don't seem that long ago). It's possibly implied in the last film that she's sick, and if so this probably wasn't too long prior to her death.
Jingle Jangle: A Christmas Journey: After the death of his wife, Jeronicus emotionally abandoned his daughter Jessica, becoming too consumed with grief and self-hatred to act like a parent, and continually pushing her away when she tried to reach out. He was convinced he'd just screw everything up and make her life worse, urging her to leave him and live her own life. So eventually, she did just that, because there was no other way for her to move forward. By the time of the main story, they haven't seen each other in some twenty years. Both have been ready to make up for quite some time, but she was still too hurt and angry to make the first move, and he was convinced she wouldn't want to hear from him. It takes the intervention of Jessica's daughter Journey for them to be able to patch things up and move on.
Kick-Ass: The hero's mother dies of a brain aneurysm at the breakfast table.
The Kid (1921): Played very sympathetically, as the mother is unwed (which, back when this movie was made, was considered shocking, especially if you were white) and doesn't have the money to care for the child herself. Note also that she leaves him in a fancy car before a fancy mansion, hoping that he'd be raised by rich people and be well-off.
The Kid with a Bike: 12-year-old Cyril is stuck living in an orphanage because his shiftless father simply refuses to care for him. After enrolling Cyril in the home, his dad moved without leaving a forwarding address, and even sold Cyril's bike.
The titular character in Norbit was abandoned at the orphanage when he was just a baby, by means of tossing him out of a moving car, that they didn't even bother to slow down, and laughing as they did so.
In An Officer and a Gentleman, Zack moves in with his father after his mother commits suicide. Dad ignores his upbringing and leaves Zack to be raised above a Philippine brothel.
Two of each in Okuribito (Departures): Daigo's father had been a Disappeared Dad for so long Daigo can't remember his face, while the encoffiner's secretary reveals she abandoned her young son over a fling. Both parents were from small towns; it's implied that they still care(d) about their children but shame prevents them from returning.
Zak from The Peanut Butter Falcon lives in a retirement home despite being a 22-year-old with Down syndrome because his family abandoned him and he had nowhere else to go.
As a child, Will Turner is found floating on a piece of wood. He told Jack his mother raised him, but she's dead now; his father spent a considerable amount of time tied to a cannon at the bottom of the ocean before making a deal with Davy Jones.
Elizabeth's mother apparently passed away when she was quite young as well.
The Burns Gang of The Proposition. Arthur, Charlie, and Mikey are brothers, but there is no reference to their parents and Arthur is implied to have raised the younger two. According to an interview on the DVD, Sam Stoat, another gang member, killed his parents.
Repo! The Genetic Opera has Shilo, whose mother Marni died just after she was born. This is only a borderline case, as her father is still present and taking care of her — unfortunately Marni's death affected him too, making him desperate to hold onto Shilo and thus ridiculously overprotective.
And then there are the Largo siblings. All three of them were bailed on by their mothers (whether Rotti had them killed or they simply left is unclear) and, combined with their distant father, they're all rather screwed up. The Expanded Universe canon material found on Myspace implies that Pavi and Amber would have been okay if their mums had survived their childhoods, but Luigi was born the way he is.
In SHAZAM!, Billy Batson escaped from over a dozen foster homes because he had been trying to find his mother that he lost in a county fair when he was four years old. When he finally tracks her down, she reveals that her parents kicked her out of the house when she got pregnant at 17, and her husband, likely a kid like her, ran out soon after. When she lost him at the fair, she realized that she could barely take care of herself, much less her young son, so she walked away when she saw how well he was being tended by the cops that found him, and decided he was better off in foster care.
In The Silence of Adultery, Michael's ex-wife Yvonne essentially abandoned their autistic son Steven after the divorce, apparently finding him too difficult to deal with. Now her only interaction with him consists of sending postcards of animals. Michael is struggling now because Yvonne was better at communicating nonverbally with Steven than he is.
Amanda Grayson is a Disposable Woman who dies on Vulcan just seconds before everyone is beamed to safety, and Spock is standing two feet away and is just too late from grabbing her. Because Spock's day wasn't going horribly enough.
George Kirk dies just seconds after the birth of his son, James T. Kirk. Oh, and Winona Kirk is 'off-planet' when her young son decides to save George Kirk's old car from being sold by his creep of a step-father by driving it (and nearly himself) over a cliff into a huge deep valley — in Iowa.
Star Wars: Luke goddamn Skywalker. He and his sister Leia both actually end up experiencing this twice. Their mother died minutes after they were born, their father spent twenty years thinking his child was dead and was completely unaware that there was a second baby, Luke finds his aunt and uncle slaughtered by stormtroopers, and Leia is Forced to Watch her homeworld get blown up while her adoptive parents were on it.
Jedi in the Old Republic were generally separated from their families at a young age to avoid attachments. Attack of the Clones makes it pretty obvious why.
Solo reveals that Han apparently ended up on the streets by the age of ten. It's not stated exactly what happened with his parents (only his father is mentioned) but they seemingly died somehow and left him an orphan.
Rey in The Force Awakens was left on the desert planet of Jakku by her parents when she was five, and is waiting for their return. For most of the film her motivation is to get back to Jakku so they don't end up missing her if they return to look for her. She eventually comes to accept that whoever left her there were actually never coming back. The Rise of Skywalker gives the full story. Rey's father was Emperor Palpatine's estranged son. Rey's parents knew about Palpatine's plan to pull a Grand Theft Me on his Force-Sensitive granddaughter, so they left her on Jakku on short notice to throw Palpatine's agents off her trail. They were murdered not long after when they refused to reveal her location.
There's no mention of what happened to Héloïse's parents. Apparently her uncle is the closest living male relative of hers though, as she's put into his guardianship. In real life no one knows, as most information is scant on her life.
Abelard and Héloïse put their son into the care of his sister after they enter monastic lives. They only see him again later when he's grown up.
In The Story of Luke, Luke's mother Sara (Lisa Ryder) left him at her parents' doorstep when he was four. She only visited him once, when he was six or seven. His father is absent as well; Sara never told anybody who he was.
In To the Bone, this is the reason Ellen is living with her stepmother and father. Her mother lost hope of her ever recovering from her eating disorder and left her shortly after she turned eighteen.
Sam Flynn in TRON: Legacy. His mother was killed in a car accident shortly after he was born. His father disappeared without a trace. Fortunately, he did have a Parental Substitute in his father's friend Alan.
In What Maisie Knew, Beale meets Maisie one last time to convince his daughter to join him in London. She refuses, after which Beale is not seen again. May be implied in the case for Susanna, as while Maisie clearly favours Margo and Lincoln for spending more time and looking after her more diligently, the last shot of Susanna is when she hugs her daughter and leaves behind some gifts for Maisie to take, meaning there is a slim chance they maintain contact with one another.
Ben: Every superhero needs a tragic family story: Spiderman's parents... Dead. Batman's parents... Murdered. Superman's parents... Exploded. I actually had the best requirements.
In Winter's Bone teenage girl Ree has to find her father, whose disappearence left the family in danger of losing their house to foreclosure and Ree's mother in severe depression and unable to take care of the family, a task that Ree has to take over.
In The Wolfman (2010), Lawrence witnessed his mother's "suicide" as a child, and if that's not traumatic enough, his father throws him into an asylum and then ships him off to live with his aunt in America afterwards.
X2: X-Men United: Judging by the sad and envious expression on Pyro's face when he stares at the Drake family photos, it's strongly implied that John's parents have disowned him (or they may have died when he was very young).