In Esther Forbes's Johnny Tremain, 1944 Newbery Medal winner and another favorite middle-school reading assignment, Rab dies at the end.
E.B. White's Charlotte's Web: Admittedly, it is a pig, not a child, who suffers the loss, but the theme of death and emotional maturity is still present. And it's still an epic Tear Jerker. (Newbery Honor, 1953)
Scott O'Dell's Island of the Blue Dolphins (Newbery Medal, 1961) kills off not only the heroine's little brother in the beginning of the novel but her friendly wolf companion toward the end. Given that these were her only companions on a deserted island, it's pretty harsh.
Lloyd Alexander's The High King (Newbery Medal, 1969), final book of the Chronicles of Prydain, takes this trope Up to Eleven. While the series hadn't exactly shied away from death before, the fifth book kills off Prince Rhun, Annlaw Clay-Shaper, the High King Math, Loino, Coll, and Achren, depicts veritable carnage in what's ostensibly a children's book, and then throws in a rape threat for good measure. The previous book, Taran Wanderer, had been the series's Coming of Age story, and had its own angsty death. Alas, no Newbery for that one.
William H. Armstrong's Sounder (Newbery Medal, 1970).
Jean Craighead George's Julie of the Wolves is a Newbery Medal winner (1973) that ends with Amaroq the Alpha wolf of the pack that adopted Julie getting shot and killed and the heroine turning her back on humanity, in part because it kills animals for sport.
A Taste of Blackberries (Newbery nominee, 1973). A boy and his pal pick blackberries: One will die from bee stings, the other will survive to eat delicious fresh berries and angst about the loss of his friend. Considered by many to be the children's book that firmly cemented the death-of-a-friend trope, it ironically did not receive a Newbery honor but was only nominated; the aforementioned Death by Newbery Medal selection Julie of the Wolves won for 1973.
The 1974 Newbery Medal winner The Slave Dancer by Paula Fox has its protagonist, already forced to perform music to exercise the human cargo of a slave ship, witness the crew tossing most all of the slaves overboard to avoid detection by authorities. While a young slave boy survives and escapes a life of slavery, and the protagonist finally makes it back home, he is so traumatized by what happened that he never enjoys music again. A colossal downer, and cynical to boot.
In A Gathering of Days: A New England Girl's Journal 1830-32 by Joan Blos (Newbery Medal, 1980), the main character's best friend dies of an illness.
Jane Langton's The Fledgling (Newbery Honor, 1981), in which the young girl (as shown on the cover) learns to fly with a Canada goose; he is shot.
Cynthia Voigt's Dicey's Song This one would have a greater effect on readers who have read the preceding book, Homecoming. The mother dies but she's been missing/hospitalized for most of the book - her death is only a confirmation of what was coming all along (Newbery Medal, 1983).
Marion Dane Bauer's On My Honor (Newbery Honor, 1987) In this one, the friend dies doing something the protagonist had promised not to do, and thus gets inflicted on tweens whose teachers think it's an important lesson.
In 1991's winner, Maniac Magee, the title character befriends an elderly zookeeper, Earl Grayson, who adopts him. They live together for a few months until Earl dies in his sleep.
1993's winner, Missing May: The titular character, the narrator's Aunt and adoptive mother, dies very early in the book, the coming of age story focuses on the narrator and her uncle dealing with their grief. Later, the narrator fears her uncle has lost the will to live from the disappointment, only to quickly snap out of it for her sake.
In Sharon Creech's Walk Two Moons (Newbery Medal, 1995), this trope is played twice. First time it's subverted because the girl's mother has been dead the whole time, she's just in denial about it. Played straight when her Grandma dies though.
Subverted in Sharon Creech's The Wanderer (Newbery Honor, 2000). Sophie and her family are sailing from USA to England to see Sophie's grandfather Bompie, whose health deteriorates as they sail. Seems that they are going to arrive just before or after his death... but ultimately he starts to feel better and they spend time together and go back.
Played with in relation to Sophie's actual parents - they were missing from the beginning, but only in the end do we learn how they died, and Sophie finally realises the fact they are dead.
Joan Bauer's Hope Was Here (Newbery Honor, 2001). The protagonist's father figure is dying of leukemia throughout the book.
A Corner of the Universe (Newbery Honor, 2003) by Ann M. Martin, where the heroine meets a long-lost uncle she didn't know she had and they become great friends. Unfortunately, he has a learning disability and is mentally ill, and commits suicide at the end. Wasn't that cheery, boys and girls?
Kira-Kira by Cynthia Kadohata (2005). Katie and her sister Lynn move to 1950's Georgia. While Katie struggles with being the only Japanese-American in her classes, Lynn seems to be becoming more popular. Eventually, Lynn gets lymphoma and dies, and teaches Katie that one should never lose hope.
Savvy (Newbery Honor, 2008). Mibs's father does not die after entering his coma, but he wakes up with amnesia and severe paralysis, making him effectively "dead" despite still technically being alive and still with the family.
Rebecca Stead's When You Reach Me (Newbery winner, 2010). Miranda slowly becomes friends with sometime bully Marcus. At the end of the book she discovers that an older version of Marcus has traveled through time to die for another child.
Anime & Manga
anohana: The Flower We Saw That Day: If there was a Newbery medal for anime, this would win one hands down. It's a sort of double-subversion layer cake with played-straight icing in the middle. The doomed character is a Cute Ghost Girl named Meiko "Menma" Honma who died years ago, but she still manages to "die" at the end by going to Heaven after finishing her Ghostly Goals, in the tear-jerkiest possible way; and her literal death in the backstory turns out to be a total Newbery Medal death in itself (at what would have been the climax of a Puppy Love-like Love Triangle plot in a Slice of Life series, poor Menma falls into a river and drowns, and her death totally changes her friends and family's dynamics).
Kill la Kill is ultimately the over-the-top tale of an abandoned, friendless teenage girl growing-up and finding her place in the world with the help of her sentient, vampiric Sailor Fuku who dramatically gives up his life for her with final words that make the coming of age theme of the story more than evident.
Suisei no Gargantia is what happens when Gen Urobuchi et al. try to write something that can be presented to the Newbery committee. This anime is a lot of things, but ultimately it's about a boy growing up and finding a place in the society. Oh, and his Robot Buddy dies in the end.
By the end of chapter 14 of the Slice of Life manga Solanin, Meiko’s boyfriend Taneda has suffered a head injury in a scooter accident. By chapter 16, he has already been buried. The cover of the first volume of the German edition shows a peaceful-looking face. When you look for that image in the manga it turns out to be Taneda while he is dying.
Bambi suffered from this after his mother got shot.
K9 subverts the trope: Dooley delivers an emotional soliloquy to what he assumes is Jerry's corpse, only to be told that patients aren't allowed in the recovery room.
The French-Canadian film La Guerre des Tuques (of the Tales For All series) took its English title, The Dog who Stopped the War from the ending of the movie. Of course the dog ends the (snowball) war by dying. Poor girl has a snow fort collapse on her. No Newbery (obviously), but several awards and nominations anyway, and an acclaimed and beloved classic to this day in Quebec.
Little Heroes. Not only does the dog die but it dies in a random way when he eats poisoned bait meant to kill a fox that is a nuisance to the local chicken farmers.
What's Eating Gilbert Grape?. At the beginning of the film it's established that Gilbert's younger mentally-impaired brother Arnie was expected to die as a young child and still "could go at any time": viewers familiar with the trope would naturally assume that Arnie would die near the end of the movie. It turns out he lives — their morbidly-obese mother is the one who dies.
Thomas Sennett (Macaulay Culkin) in My Girl (1991).
My Dog Skip looks like it's heading this way (twice, if you also count the initial possibility that Skip will starve to death in the crypt he got trapped in) but subverts it with a Disney Death. Skip does eventually die of old age at the very end of the movie, but it's more of a footnote than anything else; his owner has grown up and moved an entire ocean away by that point.
Ring of Bright Water: most of the film is about a guy and his adorable pet otter. Then a ditchdigger randomly murders it with a spade. Becomes a Tear Jerker when you find out it's Based on a True Story.
The film adaptation Paperhouse of Catherine Storr's Marianne Dreams, in which the main character never meets the best friend who dies thanks to the action taking place in Dream Land. (The novel averts the trope: both the main character and her best friend survive.)
Lampshaded in Diary of a Wimpy Kid, where Gregory is told to read Charlotte's Web, and predicts that either the girl or the pig doesn't make it to the end of the book. He never finds out what happens because he only reads three chapters.
Earlier, he said that his mom was picking out what she called "classics", the criteria of which being, in his opinion, it has to be more than 50 years old, and some person or animal has to die at the end. While most things he says are untrue and biased, this is the (unfortunately brutal) truth.
Parodied in Harlan Ellison's post-apocalyptic novel A Boy and His Dog (Nebula Award for Best Novella, 1969). The titular boy escapes with his new girlfriend to find that, in his absence, his telepathic, erudite dog has been beaten nearly to death. His girlfriend, who's kind of a jerk, makes clear that he can either save the dog, or save her. Cut to the next scene, with the dog's injuries wrapped in the girl's dress, both of them complaining about how full they are, and... something... roasting over the remains of their fire.
Spoofed in No More Dead Dogs by Gordon Korman, which starts out with the main character writing a book report about "Old Shep, My Pal", a fictional medal-winning book. He notes he knew Old Shep was going to die when he saw the award sticker, and then name-checks Old Yeller, Sounder, Bristle Face, and Where the Red Fern Grows.
Inverted in Jack London's The Call of the Wild: The dog is the protagonist, undergoing a transformation through hardship (and sometimes abuse) from dutiful pet to wild wolf, and when a Diabolus ex Machina abruptly kills his loving human master (off-screen), it allows him to make the final jump to fully wild. Not primarily for children.
Carolyn Meyer's Elliot and Win has as its climax a (extra-disturbing since the actual act is all that's offscreened) fairly brutal rape of the main character's best friend, who heretofore was a spunky, active, well-developed character.
Ginga Tetsudou no Yoru ("Night on the Galactic Railroad") - a novel by Kenji Miyazawa, made into an anime film - although the death doesn't occur at the end of the story, only the reveal of it.
The pig named Pinky dies in the climax of Robert Newton Peck's A Day No Pigs Would Die. Not an official Newbery Winner either, but the themes present in the other examples are most definitely there.
Viciously and repeatedly mocked in Brandon Sanderson's Alcatraz Series. Sanderson himself has gone on record as saying that as a kid, he hated reading because of books living up to this trope, until he found fantasy novels.
Anthony Simmons's novel The Optimists of Nine Elms (adapted into a film starring Peter Sellers) is an interesting variation. The old busker Sam's dog, Bella, indeed dies, but it's not a shock to the kids who befriend them or the reader. Sam knows and accepts this will happen sooner or later. The climax of the novel is not Bella's death, but the children managing to bury her in Hyde Park's little dog cemetery to fulfill Sam's wish that she be laid to rest there. The kids accomplishing Bella's burial—and leaving their own dog with Sam—is actually a bittersweet triumph for idealism.
Theodore Taylor's The Cay features a Magical Negro who cares for a racist blind boy while they live stranded on a tropical island, then dies in a hurricane. The book has become a classic and received a number of awards, though not an actual Newbery.
Bill Wallace's A Dog Called Kitty. The dog actually survives being mauled by wolves and makes a full recovery, only to be crushed under a falling truckload of drill pipe.
James Hurst's short story "The Scarlet Ibis", but with a physically disabled little brother.
Each Little Bird That Sings by Deborah Wiles. Slice-of-life story? Check. Dog featured on cover? Check. Award winner (not Newbery, but you get the picture)? Check. Does the dog get killed off? Oh yeah. Does the main character turn angsty and Jerk Assy over the dog's death? Surprisingly, no - that happened earlier in the novel, but it continued for a while after the dog died. Three out of four isn't bad, though.
Goodnight Mister Tom won half a dozen awards; the protagonist's baby sister dies of starvation in his arms, and his best friend is killed in an air raid.
Stone Fox, a critically acclaimed children's book about a boy and his dog entering a sled race to save his ailing grandfather's farm. The dog dies at the end.
David, the heroine's brother, in Cherie Bennett's Searching for David's Heart. For extra angst points, she blames herself for his death.
Jock of the Bushveld. Jock winds up getting shot by accident, because people were on the lookout for a chicken-stealing dog. Jock, having killed the actual culprit, returns to the farm and gets shot in a case of mistaken identity.
Mick Harte Was Here is a well-done example that shows how the narrator Phoebe and her family deal with the loss of her younger brother. It won the William Allen White Children's Book Award.
The title character in Freak the Mighty has Morquio Syndrome — or, as one character puts it, he died because his heart was too big for his body.
E. Veltistov's A Gulp of Sun pulls this off brilliantly. We do know from the beginning that somebody was killed by the cloud, but we assume this is Singaevski, the other pilot. However in the end he ends up Only Mostly Dead and Ryzh, the younger brother of hero's Love Interest and a very close friend of the protagonist dies instead.
Lampshaded in a Dilbert Sunday strip. According to Dogbert, if a movie is said by reviewers to have "powerful performances", then...
In Rule of Rose, your loyal dog Brown is the object of the Princess of the Red Rose's jealous tyranny.
Despite being predicted by several fans and even lampshaded by the developers themselves, Riley, your dog companion in Call of Duty Ghosts, averts this trope narrowly. Riley is injured by enemy gunfire and evacuated by helicopter, but he ends up just fine by the start of the next mission.
Hesh: Sorry, boy. Your job's done. You're going with Merrick.
In Portal riffs on this trope by insinuating that you develop an emotional attachment to a "companion cube" that you need to carry around to solve a level's puzzle. GlaDOS tells you that the companion cube does not actually love you, and ultimately requires you to "euthanize" it at the end of the level. She then chides you for cruelty by being so quick to destroy your only companion. Graffiti from Doug Rattmann includes tearful epitaphs to his own companion cube. This was all added after the designers noticed that testers were reluctant to destroy their cubes. The only reason the cubes were marked as special to begin with was to let players know that they'd need them throughout the level. Ultimately Portal 2 has a callback when at the end of the game, your scorched companion cube is kicked out the test facility door along with you.
Fable II has your sister in the beginning of the game and your dog at the end. With the right DLC, you can resurrect your dog.
Or you can just choose to resurrect your loved ones (which includes your dog) almost ten minutes after the dog dies. It's not like the other choices do anything important.
Haunting Ground: Hewie - a white German Shepherd dog - is introduced early on, immediately comes to Fiona's aid after she frees him, and continues to act as her sole companion and protector for the game. Mid-way through the game, he will run off into the forest to tackle a Stalker, and gets shot. If you didn't treat him well enough, he dies and you get a Bad End.
Brothers: A Tale of Two Sons is arguably one of these- though the person who dies isn't frail, they are the protagonist's (one of them, anyway) faithful companion, and their death both teaches him a valuable lesson and launches him on the path to adulthood. It feels like it's this trope.
Mother3 has Lucas getting more mature after he recovers from his mom Hinawa's death, and this again happens when his brother, Claus, commits suicide.
The Smurfs episode titled "Squeaky," in which Smurfette finds and befriends a sick mouse. With the help of Papa Smurf, the mouse is nursed back to health, but dies later after being in a house fire.
The story arc of King of the Hill when Buckley died was not nearly as touching as the episode in which his angel comes back to help Luanne get over her loss and advise her to go to college. Especially touching is the last scene before the credits when he is shown from behind walking down the street and pulls a halo from his pocket he didn't have before; the music packs an especially powerful punch.