Astro Boy, a replacement for the son Doctor Tenma lost, who died in a car accident playing with a robotic car that Doctor Tenma gave him to make up for the fact that he was so obsessed with developing a super-robot that he forgot to pay attention to his son. In one version, he was about to apologize for neglecting his son when he got the news.
Now, the incredible super-powers? If you're going to make a robot son, you would want it to be the best robot ever! And not get hit by a car. (Well, this time, his son is not going to be run over by anything short of an imperial battlecruiser.) And he already had the plans mostly finished...
Though, for some reason, in the original, the Doctor gets freaked out that his son, a robot, doesn't grow up. In other words, he got surprised that his robotic goldfish couldn't swim.
Pluto manages to one up this. Tenma realizes that the boy he created isn't Tobio, but the ideal child that Tobio never was. So Atom is in the horrible position of not being able to measure up because he's too perfect.
Of course, even though Tenma gets freaked out, he still helps Astro off and on and off again (see one example in the "World's Strongest Robot" story-arc and its remake, Urasawa Naoki's Pluto). And then in the 2003 TV version, Tenma becomes the stalker dad.
In the 2009 movie, he decides to accept Astro as a different, but equally valid son. Freakin' finally, dude.
The 1960's Astro Boy episode "Memory Day" has official replacement goldfish; when someone goes off to another planet as a pioneer, their family gets an identical-looking robot replacement. And Astro Boy has to substitute for a robot replacement that isn't ready, making Astro Boy a replacement replacement goldfish.
Honey Kisaragi in Cutey Honey, a robotic replica / partial clone of the daughter that Dr. Kisaragi lost. She was specifically told by her father that she was her own person, though.
Miracle Shoujo Limit-chan, which was something of a "sister show" to the original Cutey Honey TV anime (but much more kid-friendly and much less popular), has a similar setup. The title character, Limit Nishiyama, was nearly fatally injured and the only way to save her life was to make her a cyborg.
In Fullmetal Alchemist, Majihal creates simulacra of his lost love interest from years ago. Turns out she was alive, but he had become so obsessed with perfecting his ideal android that he refused to accept an average-looking middle-aged woman as the genuine article. Alchemist Shou Tucker is also obsessed with using human transmutation to recreate his lost daughter, whom he "killed" by using as ingredients in a transmutation experiment, which then died. (In addition, this is pretty much the reason anyone creates homunculi; the ones made for reasons other than replacing dead loved ones are exceptions.) There are also two Replacement Goldfish relationships that complement and parallel each other. The orphaned Elric brothers take on their alchemy teacher Izumi as a mother figure, while Izumi herself had a stillborn child and now accepts the Elrics as surrogate children.
In one Brotherhood OVA, the Elric brothers encounter a rich couple that lost their daughter and apparently succeeded in transmuting her back, as they see the girl completely healthy, but it turns out that, unsurprisingly, the transmutation had failed, and the couple lied to the alchemist (who lost his eyes as payment) to make him believe he succeeded, and the girl was, in reality, an orphan they adopted because of her uncanny resemblance to their late daughter.
In one of the Yonkoma, Van Hohenheim accidentally drops the flask containing the Homunculus, killing it. He replaces it with a goldfish.
Rei Ayanami from Neon Genesis Evangelion is partly cloned from the DNA from Gendo Ikari's wife, Yui, and is therefore Gendo's replacement goldfish for Yui. She has also died and been resurrected twice, which would make her a replacement goldfish for herself, and she is the surrogate host for the soul of Lilith because she has no soul of her own. Furthermore, Ritsuko considers herself to be a substitute of sorts for Rei. Meanwhile, Gendo considers Ritsuko a substitute for her mother Naoko, however, his feelings for both of them were equally cynical in nature. He didn't love either of them so much as he needed access to their skill sets and one was just as good as the other. The Dummy Plugs, which are intended to replace pilots, are based on Rei and Kaworu's personalities. And don't even get started on the whole thing with Kaji, Misato, and Misato's father.
Rei could also be considered Gendo's replacement for Shinji. In one of his angry inner rants, Shinji even says as much. The fact that Rei was the name Gendo had planned on giving Shinji, if he had been born as a girl, seems to support this.
An old man in the anime of Rozen Maiden convinced himself the boyish doll Souseiseki was his child, Kazuki.
Variation: Fate Testarossa from Magical Girl Lyrical Nanoha was (unknown to her) supposed to be a replacement for Alicia Testarossa, the daughter of Precia Testarossa. Unfortunately, even with Alicia's memories, Fate was not a perfect copy (the Movie mentions that unlike Alicia, she's not left-handed and has different magic potential). In the end, she unwittingly became merely a tool to help Precia resurrect Alicia, while her inability to mimic the original led to much suffering on her part.
Her adopted son was in a similar position: he's a product of the same cloning tech that created Fate. It seems to have improved somewhat in the interim, as he's never mentioned to be different from the original Erio. He was taken away from his "parents" when the Bureau found out about his origins. One of the reasons Fate took him in was to try to prevent him from going through the same kind of pain she did as a child.
In the Pokémon CD drama short story "The Birth of Mewtwo," the scientist who was working on Mewtwo was attempting to recreate his daughter at the same time. He was successful only in creating a clone that would live for only a year in a tank.
There's also Jessibelle, James's psychotic would-be fiancée who looks almost identical to Jessie. James drifted toward a life of crime (and to Jessie) partially out of spite for his arranged engagement with Jessibelle as a child.
In The Big O anime, R. Dorothy Wayneright was an android created as a surrogate for the deceased daughter of her creator.
It should be noted, though, that he eventually understands what he is doing to Yuzuki and decides to stop updating his sister's personality into her. Also, the whole thing might be insane if it came from a scientist with no interest for ethics, but it's understandable since he's a lonely 12-year-old who needs some kind of emotional protector.
An unusual case crops up in xxxHOLiC when it turns out the reason Watanuki was even born was because the universe generated him to fill the void Syaoran left behind when he was removed from his own timeline. It's unusual because this isn't about filling an emotional void, just a literal one.
In Touka Gettan, Yomiko considers Touka to be her dead daughter.
Eris did this with her dead love Rezo, giving us Copy Rezo.
Suzu in Hotori - Tada Saiwai o Koinegau is a robot replacement for a couple who has recently lost their son to illness, and struggles with the question of whether he has an identity of his own. The "doctor" who's overseeing the process of implanting the dead boy's memories into Suzu also has a terminally ill daughter, but (perhaps wisely) decides against getting a Replacement Goldfish because he's got enough experience with the robot doubles to know that however good the replacement is, it will never really be her.
There's a trace of this in Sonic X where Shadow the Hedgehog, despite his current outright abhorrence of humans, chooses to save Chris Thorndyke from an exploding island after envisioning him as Maria Robotnik (it's all in the eyes, apparently). Somewhat subverted as it does not stop him from bashing the kid about a bit several episodes later.
Played with in the second season of Gundam 00. Neil Dylandy, the original Lockon Stratos, has a twin brother named Lyle, who eventually takes up his brother's place as Lockon in Celestial Being. He grew into being his own person by acting like as much of a Jerkass as he could when he first came to Celestial Being, purposely failing to deliver during battle, and refusing to feel vengeful when everyone expected him to. Only later does he actually put his heart into filling his dead brother's shoes, and it was when he was trying to save Katatron, the group for whom he was acting as a Double Agent. Later, he says that, as a child, he had himself sent to boarding school to get away from the comparisons and laments the fact that he will never live Neil down.
An episode of The Third features the superweapon Gravestone, whose creator made it in the image of his dead son and ended up trying not to use it for that reason.
In Pet Shop of Horrors, an early chapter of the manga which became the first episode of the anime involves the Count selling a "rabbit" to a pair of distraught parents - a "rabbit" who looks exactly like their dead daughter, Alice. They take her in and treat her exactly the same as their own daughter, with disastrous results. It turns out that the "rabbit", when fed sweets, "gives birth to" (is eaten from within by) dozens of killer rabbits, each of which go forth, kill, eat, and "give birth" to more killer bunnies until the town is overrun.
Quite a few Pet Shop of Horrors chapters deal with D giving a pet as a replacement for a lost child, spouse, or family member. Almost all of them appear human to the owners and (thankfully) they don't all end like Alice the Rabbit did. In one chapter, D is visited by a man whose famous fiancée just died and gives him a mermaid that looks just like her...a mermaid which enchants and seduces him before devouring him. Another chapter has Leon's younger brother Chris bond with a Maya bird which appears in the form of Chris and Leon's deceased mother, giving both a chance for emotional release before finally dying of old age. In fact, it was in that chapter that D comments on how the pets in his shop will deliberately take the form and role of whomever the owners want, including lost loved ones.
In Sola, we find out that the protagonist, Yorito, is actually a replacement made out of paper by Aono to replace the REAL Yorito, who died sometime in the feudal era in a landslide. Using her paper manipulation abilities as a yaka, she basically planted dead!Yorito's personality and memories into origami!Yorito. The whole thing is a bit disturbing when you think about it.
Near the end, Aono uses her powers to control Yorito when he tries to intervene in a fight. Yorito calls her out on this and points out that she would never have done that to the real Yorito.
Shiina in Narutaru gets to be this in a very strange way in the manga. She's a replacement for herself after she is killed by a fighter jet; it's basically the handiwork of her real Mon, the Earth itself, because she still has to fulfill her role in what will become of the world.
Not to mention that if you believe the theory that Shiina drowned in the very first chapter, the Shiina we see throughout most of the manga is a replacement of that Shiina. And it's possible that there were other examples even before then. You gotta love Narutaru.
In Cosmo Warrior Zero, the new first mate, Marina Oki, looks EXACTLY like Captain Zero's late wife.
The Manwha (and movie) My Sassy Girl is about a man who meets a seemingly deranged woman who forces him to act like her deceased lover ("No soda, coffee!"). By coincidence, the dead lover is the man's cousin.
The second season of Code Geass has Rolo, who was inserted into Lelouch's modified memories by Emperor Charles as part of a backup plan should Lelouch ever realize who he truly is.
In Fruits Basket, Yuki sees Tohru as a replacement mother figure.
Kyo sees his sensei as a replacement father; the man in turn sees Kyo as a son.
A story in Mermaid Saga has Mana and Yuta meet a woman and her young son who turn out to be both immortal and together since World War II. Turns out, the boy isn't the woman's biological child. He became immortal first and offered her a chance to eat the mermaid's flesh and be with him. She accepted because her own child died and she saw the boy as a replacement.
In the Full Metal Panic! novels, this can be a rather disturbing (and possibly implied) view of the two (male) twins that Gauron took in. It's revealed that Gauron had actually wanted to lure and take Sousuke in the first time he saw him, giving him a "dark smile" (read: rapeface), and, later, even coming out and saying that his plans for Sousuke had been less than pure (hint: it involves raping him). Later, Gauron ends up taking in two male twins that he tells Sousuke "were quite similar to you". It gets worse: The twins are both Asian (like Sousuke), and they are described using similar terms to Sousuke's physical looks ("slender" build, around the same age, with a similar sort of haircut, and one of the twins even uses the same kind of gun Sousuke normally uses - an automatic pistol, which was also why Kaname knew how that gun worked better than if he had been using a different kind).
Happens twice in RahXephon. The two main leads, Ayato and Haruka, inadvertently seek out a Replacement Goldfish for one another after they're separated across time by the arrival of the Mulians. Haruka starts dating Ayato's twin brother Itsuki, and Ayato becomes infatuated with a girl named Reika who's actually a spirit that's adopted the guise of Haruka because Ayato misses her that much.. Eventually, they are reunited and everything is set right with the help of the titular Giant Mecha.
Game X Rush features the 'replacement child' type, with Miyuki's damaged mind believing that Yuuki was her son, Memori... and that anyone who tried to say differently was clearly trying to take Memori from her, and thus should be stabbed until they're dead.
Considering how the writers are Magnificent Bastards they never let us know whether or not she failed and if Pazu was or was not killed and replaced.
In Vampire Knight, after noticing Yuuki's resemblence to her mother Juri, Yuuki's uncle Rido (who was in love with Juri) changed his plans from devouring Yuuki to keeping her as a substitute for Juri.
In the original TV series of Hellsing, studio Gonzo reveals in an interview of Newtype that the reason why Alucard turns Seras Victoria into a vampire was because 'her eyes' reminded him to 'Integra's' when she was a young girl. This is never brought up in the series, though they do make an emphasis on her eyes when he's about to shoot her.
This shows up occasionally in the Dolls series with people trying to use the titular Ridiculously Human Robots as Replacement Goldfish. In one story, a little boy who is neglected by his mother is given a Doll that looks exactly like her for Christmas. When the boy tells his real mother that it's okay that she ignores him because he doesn't need her anymore, she has a Heel Realization — which might have been the Doll's creator's goal all along. In another story, a woman who lost her son when a Doll accidentally drowned him in the bathtub and formed an anti-Doll terrorist group in response and begins to see the enforcer Doll (that looks like a young boy) that was sent to stop the group as a replacement son. The inventor of the Dolls nearly went through with this after his wife — who helped invent the Dolls — succumbed to a neurological disease that left her a listless shadow of her former self. In his grief, he designed a Doll that looked exactly like her and uploaded her memories into the Doll. When the Doll is activated and greets him with his wife's voice, he embraces it in joy — but stops when the Doll calls him "Master". Coming to his senses, the man devotes himself to taking care of his invalid wife.
An episode of Black Jack 21 has the good doctor (and his assistant/adopted daughter/wife, Pinoco) befriend a young guy living in a developing country. Originally one half of a pair of identical twins, his brother was adopted as a Replacement Goldfish for a wealthy man whose child (who looked identical to the brothers) perished in the same flood that rendered the twins orphans. The man hid the death of their child from his wife, and thus couldn't adopt both of them, forcing the twins to be separated, and the adopted twin to act like the long-dead boy in order to avoid breaking the heart of his adopted mother. (On top of this, she was injured during the flood and was left with a delicate health.) Cue his twin brother winding up mortally ill and in dire need of a kidney-transplant...and only one compatible donor in the city.
In Tenshi Ni Narumon, Kai knows that Natsumi, who he is in love with, sees him just as a replacement for her dead brother Fuyuki, who Natsumi had obsessed over constantly since his death. He eventually decides that, for her own good, it would be the best if they parted ways.
In the original, 1969 Himitsu no Akko-chan series, Atsuko "Akko-chan" Kagami, the main protagonist, has to ask, for a school assignment, the origins of her name. She discovers that Atsuko was actually supposed to be her older sister who was stillborn. Being born a little girl, the "younger" Atsuko was given the name already used for her dead sibling, with no one ever mentioning that until she asked first.
Kagome of InuYasha has major insecurites over the fact that she may be the title character's Replacement Goldfish for his lost love, Kikyou, aka Kagome's self in her past life. As the love plot thickens and Kikyo is brought back to life, it continues to play into Kagome's inferiority complex that Inuyasha will eventually return to her.
An interesting variation in Tenchi Muyo!: In the OAV timeline, Sasami's connection to Tsunami began when Sasami, as a toddler, fell from a near-fatal height to the base of Tsunami's tree. To do so, Tsunami saved her by combining their lifeforce to heal the little girl; however, Sasami didn't understand and was afraid that she might just be Tsunami's copy of the real girl, and so carried the secret for years for fear of losing her family's love. When it's revealed, however, Tenchi and the other girls didn't exactly care, and Ayeka openly told her that she was still Sasami.
In Mawaru-Penguindrum, Ringo Oginome actually aims to become one of this in regards to her deceased older sister, Momoka, even when her parents had not asked her for anything by these lines. By episode 14, she has decided to not go through it.
Family Compo revolves around this. The adult protagonist is taken in by his aunt (who is near-identical to his deceased mother), her husband, and their daughter. The protagonist has romantic feelings toward his cousin but other than that they act like a typical family.
Midori Wakatsuki's foster parents in Eden No Hana adopted her to fill in the blank left by the death of her biological daughter Reika. Her mentally-broken foster mom treats her with relative kindness, but calls her by the dead little girl's name and acts as if Midori was the real Reika. Her issues are made worse by the fact that her stepbrothersexually abuses her.
Franken Fran has one truly brilliant subversion of this trope. One story follows a robotics expert asking for Fran's help in putting his dying wife's personality and memories into a robot program so he never has to lose her. In usual ironic fashion, he uses the program to make his new robot model, gets rich by selling them and starts to mess around with other women while ignoring his wife's robotic form because he doesn't believe it's her anymore. In comes karma like a steamroller, with a large army of robots with his wife's personality eventually become far too lonely and all go after him, unaware of their own strength and nearly kill him. When Fran enters the picture again, a robot remaining asks that he be saved so they can be together forever, and Fran figures there's only one way to do that properly. She turns him into a robotic program as well, that becoming his second model and him being so scared that he becomes a floor mat to the innocent wife robot.
Beluna, one of the maids in The Voynich Hotel is actually a simulacrum made by Elena, AKA Lachrymarum. The latter arrived too late to stop the beheading of the original, and used what was left to make the former.
Played with in Kyousogiga. When the priest Myoe if forced to leave the realm he created, he makes his adopted son Yakushimaru into a replacement goldfish for himself. The second Myoe understandably has very mixed feelings about this.