Berserk: Guts's adoptive father Gambino told him this word for word when he triedto kill him. He's referring to Sys, Gambino's lover, who died from the plague just three years after they took Guts in. He blames this on Guts due to a superstitious belief that his being born from a corpse makes him bad luck, which fueled a hatred that had previously led him to sell the kid to one of his men as a child prostitute for three silver coins.
Light:*sighs* I wish Rem had survived instead of you.
In a flashback in H2O: Footprints in the Sand, Hinata's grandfather wishes that Hotaru, whom we had known to this point as Hinata, had died instead of her sister. So much that he forces her to steal her sister's identity and renounce her room, her hobbies, and anything that made Hotaru distinct from the real Hinata. No wonder it hurts when the townspeople gossip that it was better that Hinata survived and Hotaru died.
Higurashi no Naku Koro ni: This pushes Shion over the edge in Meakashi-hen, when she thinks that her yakuza family killed her boyfriend and wishes that it had been his little sister instead, whom she never liked anyway. When her Roaring Rampage of Revenge gets to the sister, we get the most disturbing murder scene in the entire series, followed by one of the biggest tearjerkers.
SHUFFLE!: Eight years prior to the story, both of Rin's parents and Kaede's mother are killed in a car accident. Kaede became traumautized from the incident, losing her will to live. Rin overhears the doctor say that she needs a reason, any reason, to live. Rin then goes to Kaede and tells her that on the night of the accident, he was lonely and phoned his parents, asking them to come back. Since his parents and Kaede's mother rode in the same car, he essentially told Kaede that it was his fault that her mother died. This causes Kaede to snap out of her stupor and she tries to strangle Rin to death.
Rin manages to escape, but since Kaede's father has taken Rin into their home, Rin must constantly put up with Kaede's deep hatred of him. While putting on a front of being friends with Rin around her father, Kaede does such things as vandalize Rin's room, drop a box-cutter on his face so that it slices his eye while he's coming up the stairs, locks him out of the house when its raining and goes outside to meet him where she tell him "I don't understand. Why did my mother have to die, while someone like you still gets to live? I wish you were dead. I mean it! Just die!" Once she finds out that it was actually indirectly her fault that her mother died (she had fallen ill, and her father asked her mother and Rin's parents to come home) she then spends the next few years of her life completely devoting herself to Rin in an attempt to make up for how she treated him during their childhood.
In Skip Beat!, it's a little unclear how the car accident death of Hizuri Kuon's older friend Rick came about, sending him into an Angst Coma, but a large part of the reason it hit him so hard is that a blonde woman attached to them both expressed this sentiment and called Kuon a murderer. Even if he was (illegally) driving the car, it would have been a completely accidental vehicular homicide, since Rick couldn't even get the kid to do violence to a chicken because of his excessive empathy. And it doesn't look like he was driving.
He only got out of the Angst Coma by turning into Tsuruga Ren. And when he almost got into a car accident when a little boy ran in front of his stunt vehicle, he suffered flashbacks.
A Cruel God Reigns: Played straight and is a literal line from Jeremy when he is standing at Sandra's grave. He says that Greg should have died instead, as Greg is still hospitalized at this point.
In Naruto, Neji essentially has this attitude toward Hiashi, and to a lesser extent, Hinata, and the cause of his resentment toward the head family is blaming them for his father, Hizashi's, death. When Neji was four and Hinata was three, Hinata was kidnapped, and her father Hiashi killed the kidnapper, an important dignitary from the Cloud Village. The Cloud Village then demanded the murderer's death, and the head family had Hizashi die in Hiashi's place, although it later turns out that Hizashi did so willingly.
In Attack on Titan, Ymir indirectly expresses this sentiment by saying how it's unfortunate that Armin is the Sole Survivor of his patrol group, and wasn't worth the sacrifices of Eren and the rest (Eren later survived by turning into a Titan, but no one knew this at the time).
In Hellblazer, John Constantine gets this a lot. A lot of times, the people saying it are right.
Watchmen: Rorschach's backstory reveals that his mother was a prostitute, and as a child he interrupted her while she was busy on the job. Her john left, paying only a token amount, and she descended angrily on her son — slapping him, shaking him, and shouting "I should have had that abortion!" As an adult, when he was informed of his mother's death, he responded with a single word: "Good."
In the Jack Chick tract "Happy Hour," Jerry's daughter Janice, after breaking the bottles of alcohol he bought with the grocery money, tells him "We wish you'd died instead of Mommy!" which is more understandable than most instances, since he pushed her over and caused her death from a heart attack when she tried to stop him from using their last money at the bars. This being a Jack Chick tract, Jerry repents and is Easily Forgiven by his children in the end.
In the last arc of Runaways, an accident results in an explosion that hits Old Lace and Klara. Old Lace covers Klara, shielding her from the blast, and apparently dies as a result. Throughout the arc, Chase makes it abundantly clear that he wishes Klara had died instead. Later, when the team shows up in Avengers Academy, it's heavily implied that Klara's developed such severe Survivors Guilt that she blames herself for the accident.
Dick: Bastard! It should have been you! It's your fault! If you'd told Two-Face who you were at the circus, they'd still be alive!
In fact, Bruce had tried, yelling out "Harvey! I'm Batman!" just beforehand, but no one could hear him over the panic.
Batman: If Bruce Wayne could have given his life for your family, he would have.
The Johnny Cash biopic Walk the Line shows how Johnny's father blamed him for his brother's death, and didn't respect his musical accomplishments.
In Walk Hard: The Dewey Cox Story (an over-the-top parody of Walk the Line and other musical biopics), his own father tells him "The wrong kid died." Repeatedly. He visits Dewey in rehab just to reiterate this, he sings it as he does fieldwork...
In Alaska Sean says to his father's face how he wishes he had died and not his mom.
In Stand by Me, Gordy was never as understood or loved by his parents as his athletic big brother, who was killed in a car crash a year before the film. He has a nightmare at one point, being at the funeral, and hearing his father say, "It should have been you, Gordon." While this might be All Just a Dream, Gordy mentions another detail about the funeral a moment later as it were true...
Unfortunately, parents don't need to use words to make such a message understood.
In the Star Wars Expanded Universe, Han expresses this general sentiment, if not the exact words, to his son Anakin after Chewbacca's death.
It's worth noting that Faramir's question was worded that if one of them had to die, would Denethor have preferred Boromir to live. Denethor's answer is based on his belief that if Boromir was still alive, Minas Tirith would have a better chance of surviving the impending attack.
His wording in the book is "Yes, I wish that indeed, for Boromir was loyal to me and no wizard's pupil... He would have brought me a mighty gift.". At least in the film, he hesitates to say this to Faramir, and his voice trembles. In the book he has no such hesitation. The full line is in the deleted scenes.
Note that, buried in the Council of Elrond scene in the book, Boromir explains that it was Faramir who had the dream, and that Boromir followed the vision because Faramir was... not so ruggedly heroic as his brother. Leading to Denethor being actually rather justified in saying that Faramir "should've" been the one to die as he was the one being called. But on the flip side, Faramir shows exceptional resistance to the ring's temptations. How far would the Fellowship have gotten, if it had been Faramir and not Boromir who went along?
Faramir wanted to follow the vision himself, but Boromir claimed the quest out of Big Brother Instinct and Denethor approved.
It also needs to be noted that Boromir was trying to get the ring for his father. Faramir may also have been helped by the fact that he was told his brother attacked an innocent hobbit like a madman for a ring despite the ruinous power it holds.
In Harry Potter and the Prisoner of Azkaban, Wormtail tries to justify to Harry, Sirius and Lupin his betrayal of Lily and James Potter, claiming that Voldemort would have killed him if he hadn't told him where they were. Sirius shouts furiously, "THEN YOU SHOULD HAVE DIED! Died rather than betray your friends, as we would have done for you!"
The others would have chosen death over betrayal, so yes, Sirius' attitude is very much justified. (All the more seeing how he's had to carry the guilt of suggesting Wormtail be the Secret-Keeper needed for the Fidelius charm to work.)
Late in Aunt Dimity's Christmas, Lady Haverford admits to provoking this in her brother Christopher Anscombe-Smith (known as variously as "Kit" and "Smitty"), the vagrant who collapsed in Lori's driveway. He had questioned the glory of their father's actions in WWII, and the father compiled a memoir of his unit's bombing raids in an effort to explain himself to his son. Some ten years later, the father hanged himself and Lady Haverford blamed her brother for causing the suicide. The brother took this accusation to heart, gave away his wealth, lived as a vagrant, and performed a variety of good deeds along the way.
A Song of Ice and Fire: Catelyn Stark's greatest moment of bitchiness in A Game of Thrones has her throwing this at Jon. Though the character at question wasn't dead just yet.
Expanded on in the HBO adaptation where she's shown as hating Jon and admitting she prayed to the gods for him to die... but also hating herself for being such a horrible person as to ask for the death of a child. And yet, she's so bitter that she can't bring herself to change.
Also implied in-universe that a big part of the reason Tywin Lannister hates his dwarf son Tyrion is because Tywin's wife—the only woman he ever loved, the only person who made him something other than the ice-cold sociopathic bastard that he became—died giving birth to Tyrion. The fact that Tyrion was a dwarf (historically, deformation was considered a sign of evil) only made things worse.
This is also part of the reason Cersei hates Tyrion so much, with this aspect being more pronounced in the show than in the books.
A more poignant example appears in the Prequel, Tales of Dunk and Egg where at the end of "The Hedge Knight", Prince Valarr grieves for the loss of his kind father, the beloved Baelor Breakspear, and wonders how a hedge knight like Dunk gets to live instead of the man who had the potential to be the greatest of the Targaryen Kings.
1984: At the end, Room 101's purpose, at least for Winston, is to make him truly wish the torture on his loved ones instead of himself.
In Henry James' novel Washington Square, the father of heroine Catherine Sloper hates his daughter because his beloved wife died while giving birth to her. He spends the rest of his life belittling and tormenting her emotionally.
Fable: In the novel based off the video game, the main character is called into his dying mother's bed chamber where she tells him that she's happy that he survived the balverine attack instead of his brother, since he has prospects and business sense whereas his brother was just a dreamer. Only problem is that she's remembering it backwards and thinks he's his dead brother.
Vorkosigan Saga: After the birth of Miles, near the end of Barrayar, Count Piotr says that he wishes that Mad Emperor Yuri's death squad had killed Aral, instead of his older brother. This is the final straw in their deteriorating relationship, leading to a 5 year estrangement.
Satirical variation: British columnist Victor Lewis-Smith has been quoted as saying "The Beatles are dying in the wrong order." George Carlin wrote something similar: "The wrong two Beatles died first." Comedienne Judy Tenuta once joked that John Lennon's assassin Mark David Chapman would have been considered a hero if he'd aimed two feet to the left.
Stephen King's Duma Key, features divorced wife Pam saying this to Edgar when their daughter is killed.
Another Stephen King example comes in The Eyes of The Dragon where the universally beloved Queen Sasha dies giving birth to the rather useless Prince Thomas. Thomas imagines that not only his father, but pretty much everyone in the kingdom is thinking, "We lost your mother, and we got you instead?"
In Haruki Murakami's Norwegian Wood when one of the characters, Midori, is telling the protagonist her backstory, she talks about her mother dying and her father saying to her and her sister he'd rather they died than her, and how on one level she admitted the sentiment was very nice to her mother, but on the other it wasn't something a father should say to his daughters.
There is an old children's horror novel where the main character's name is Matt, and his apparently perfect older sister, Penny, was murdered ten years ago. He often gets into trouble, and during one incident, his mother tells him, "And poor Penny's the one who had to die!" Later on she tries to make it up to him, but he never forgets how badly it hurt him to hear it. Of course, it turns out that Penny wasn't so nice and kind after all, and actually died in the attempt to kill a four-year-old Matt...
From Adeline Yen Mah's memoir Falling Leaves. Jeanne openly wishes that her daughter, Susan, had died instead of her favorite child, Franklin, a brat and a bully who died from bulbar polio contracted after gorging himself on unwashed strawberries. The resulting quarrel leads to Susan's disinheritance.
In A Yellow Raft In Blue Water, it's the treatment Christine feels she got when she was attending the wake for her brother Lee's funeral, because she talked him into joining the army, which during his time of service he was sent to Vietnam and was reported as MIA.
Inverted in The Last Hope, where Graystripe tells a recently-killed Firestar that he would have taken his place if he could.
In Inkspell, after Dustfinger makes a deal with the White Women to offer his life in exchange of bringing Farid back, Roxanne, Dustfinger's wife, furiously tells Farid that he ought to be dead instead of Dustfinger. Why? Because Roxanne wouldn't let Orpheous use Word Power to try to bring him back, and Farid disagreed with her. This made its way onto the Dethroning Moment of Suck page.
A non-human example from Mockingjay: Katniss finds her sister Prim's pet cat in the ruins of District 12 and wonders why, if one of Prim's pets was still alive, it had to be the cat (whom Katniss had always hated) rather than the goat (whom Katniss thought was both sweet and useful).
In Andre Norton's Storm over Warlock, when Shann finds Thorvald in the dreams, and Thorvald registers him, Thorvald says that Garth had died in the Throg attack, and Shann should have died too. On the other hand, he is still in the grip of the dreams at the time — as soon as he realizes that Shann is really there, he is warm and welcoming.
In Mercedes Lackey's Last Herald-Mage Trilogy, Vanyel, who is grieving and shocked from the loss of his lover Tylendel and being landed with half-a-dozen psychic gifts at once, gets this reaction from the Herald who is watching over him. While the man would never have said it out loud, Vanyel has just become an extremely powerful telepath, and hearing those thoughts pushes him over the edge and into a suicide attempt.
Live Action TV
In Awake Rex says this of his father, though in a realistic spin, he's ashamed of it.
Dexter: Astor says this when she finds out Rita's dead.
Not death, per se, but Freddie's mom does this quite a few times after Freddie risks his life to save Carly's in "iSaved Your Life".
Carly: How is he?
Mrs. Benson: Broken. Damaged. But I see you're fine, isn't that nice?
And this gem.
It should have been yoooooou.
LOST : Benjamin Linus's father expressed these sentiments to Ben — that he'd wished Ben had died rather than his mother.
Millennium: In the third season, Mr. Miller tells Frank that he wishes Frank had died instead of Catherine. This is a fairly understandable case, as almost any family would choose their daughter over their son-in-law if push came to shove.
Soap: Elaine Lefkowitz, Danny's first wife, had this ("Why couldn't it have been you?") said to her by her father after her mother and sister died. This made her distrust everybody and become the spoilt, unlikeable woman that she was when she married Danny (fortunately she becomes nicer). Unfortunately, she dies shortly afterward.
Xander implies this in a mild way in the Buffy the Vampire Slayer series finale when Andrew tells him that Anya saved his life, sacrificing herself in the process. "That's my girl...always doing the stupid thing".
In I, Claudius, Claudius' mother tells him flat out that she wishes he had died instead of his more accomplished brother (who was poisoned by his grandmother's agents.) Of course, if Claudius hadn't been acting like a complete fool, he would have probably been likewise targeted for death as a young man, since his political beliefs also ran counter to his grandmother's.
In the first episode of Arrow, Laurel blames Oliver for her sister's death and tells him that she wishes he had died in her place. He wished the same thing too.
In The Vampire Diaries, Damon and Stefan tell Matt he should have died instead of Elena in 4x01.
Eminem: When he was in his late teens, Marshall Bruce Mathers III (Eminem) was told by his mother over the phone that he should've died instead of his beloved uncle Ronnie. On the day of Ronnie's funeral. One part of the song "Cleaning Out My Closet" is dedicated to blasting her for this.
''Remember when Ronnie died and you said you wished it was me? Well guess what, I am dead, dead to you as can be!"
Jeselnik: It's been a rough year for comedy. Not only did the world lose Greg Giraldo...*applause from audience*...but even worse, it kept Jeff Ross.
The day after Patrice Oneal died, fellow comedian Colin Quinn, while appearing on an impromptu memorial show on SiriusXM's Opie And Anthony, noted that he received several tweets from Patrice's fans wishing that he had died instead. He went on to say that Amy Schumer, who made several jokes at Patrice's expense during Comedy Central's Charlie Sheen roast, received messages stating that they hoped she got ovarian cancer.
In Equivocation by Bill Cain, this colors the relationship between Shag and his daughter Judith: her twin died as a child, and he can't help wishing that she had been the one to die instead.
In Tales of Symphonia, during Zelos' "night in Flanoir" scene, Zelos reveals to you that his mother was shot by an arrow that was meant for him. His mother hits the point home with: "You should have never been born."
A sentiment related to this trope comes up when Pietro escapes from the Asgard-area Human Ranch, only to be reduced to a nearly mindless shell of his former self, and his escape indirectly leads to the Desians attacking and razing Luin, taking the survivors to the ranch. When Sophia is reluctant to have Pietro show the party how to re-enter the human ranch, Sheena angrily reminds her that because of him, many people from Luin lost their lives, and the least he can do is help.
In .hack//G.U., this happens to Sakubo's player Iori, who is an Ill Boy in real world. Frustrated at her son's condition, Iori's mother wished the one who was alive was Iori's stillborn twin sister, Sakura.