Mr. Zsasz from the Batman comics carves a tally mark into his body every time he kills someone. His whole body is covered in them.
One Judge Dredd short story centered on a man trying to become famous by growing the world's largest nose — and falling afoul of a collector of body oddities, who wanted to mount the nose on a plaque. Eventually, Judge Dredd finds his hideout, with an extensive collection of heads, arms, and other parts, each one notable in some way — and each one taken forcibly and likely fatally.
Perhaps the strangest example is consul Enshu Atsukau from Sillage: he uses his telepathy to seduce females of various species. The addition to his harem is marked by a connection to a machine that links their neural systems to his in a permanent empathic link — which requires one of their eyes to be replaced by a cybernetic implant. The machine is surrounded by row upon row of small jars with their removed eyes floating inside.
Films — Live-Action
Captain Love in The Mask of Zorro keeps his enemies' body parts in jars of alcohol and drinks from them, supposedly to gain insight on their strategies. This becomes much creepier when he invites Alejandro to drink from the jar containing his own brother's head.
In Cube 2: Hypercube, a man who's been in the hypercube for some time starts killing and eating others and wearing their watches/dog tags as souvenirs.
The Predator collects skulls from its prey, including intelligent ones. We get to see a very impressive display at the end of Predator 2, including the elongated skull of a Xenomorph, laying down the foundation for the Alien vs. Predator franchise, and the Predators give Harrigan a flintlock pistol.
General Grievious carries a collection of lightsabers from the Jedi he has killed.
Boba Fett kept Wookiee scalps on his belt as trophies of his kills.
Universal Soldier starts out with a rogue soldier killing Vietnamese civilians — to emphasize his insanity, he wears a necklace of human ears.
The main villain from Battle Beyond the Stars collects limbs from people he killed - and use them to replace his own. This comes back to bite him when one of his victims was a member of a hivemind who could still control the arm and tried to strangle him.
Narrowly averted in the Holocaust drama Amen, when the SS Doctor shows up at Kurt Gerstein's house and offers to show his children a "genuine Judeo-Bolshevik skull". Gerstein is horrified and tries to stop him, though he turns out all he's carrying is an ape's head made of chocolate. But by this point of the film, neither Gerstein nor the audience would have put it past him.
The south gate of the Darklands city of Kaag is adorned with the huge skull of Nyxator (the Crystal Dragon Jesus figure of Magnamund), and covered by the dragon's preserved hide, as a trophy for the Darklords.
The famous French short story "La Main" ("The Hand") by Guy De Maupassant is about a hunter who cut off the arm of his enemy, dried it in the sun, and hung it in his living room. Later, the man is found dead, with marks on his neck showing he was strangled... and the hand in the living room is missing.
In one short story, an assassin kills a man who turns out to be a serial killer (which is a part of a larger plot between gods — Loki has survived to modern times and uses serial killers to gather human nails that he needs to build his ship) — the assassin enters the man's house and starts retching when he finds a whole wall of jars full of eyeballs staring at him.
Bennat Ladradun in Tamora Pierce's Circle Universe keeps a shelf full of mementos that he takes from fires in which he makes a difference (he is a semi-professional firefighter). However, excepting one (his dead wife's hand, complete with matching melted ring), they are actually mementos from the fires that he set.
And over in her Tortall-verse there's George from The Song Of The Lioness books who often cheerfully references his collection of ears. Unusually for the trope he's one of the good guys - indeed he's one of the romantic leads and the man our protagonist ends up marrying.
The Silence of the Lambs. Buffalo Bill collects parts of the skin of his victims to make a woman suit. This is actually lampshaded when Clarice mentions that most serial killers keep souvenirs of their victims.
The Tattered Prince is a mercenary leader known from wearing a cloak stitched from rags of cloaks of his defeated enemies.
One of the barbarian leaders wears a necklace of ears from defeated enemies. Unusually for the trope, all of them had been left alive — they can come back to challenge her and get their ears back if they ever find the courage.
In 1632, Gunther Achterhof of the Magdeburg Committee of Correspondence was said to carry around the ears, noses, and private parts of two soldiers he had killed before joining the CoC, in revenge for the killing of his family by an army passing through the area.
In the Warrior Cats series, members of BloodClan, a group of vicious strays in the city, collect teeth from cats and dogs they have killed, wearing them as Spikes of Villainy on their collars. (This started when their leader, as a young cat, attempted to use a loose dog tooth he found to try getting his collar off, only to get the tooth stuck. When others asked about the tooth, he claimed he killed a dog and took the tooth as a trophy, and from there the idea took off and became true.)
In Harry Potter, Voldemort has this trait. A flashback shows that he did it even as a child, stealing keepsakes from children he had magically tormented. This habit results in a minor Nice Job Fixing It, Villain moment, as it allows Dumbledore and later Harry to deduce the locations and identities of Voldemort's Horcruxes.
In the Redwall series, the vixen Silvamord wears a skirt made of the tails of other creatures. This would be roughly the Redwall world's equivalent of wearing a skirt made of people's arms or something. Her husband wears a wolf skin, which is just as bad, and a few other characters wear their enemies' skins or teeth.
"There had been that... bad business with that little girl and those men over at Dolly Sisters, and when Sam had broken in to the men's lodging he found one of them had stolen one of her shoes, and [Lady Sybil had] heard Detritus say that if he hadn't been there, only Sam would have walked out of the room alive..."
In A Civil Campaign Miles is showing his fiance around Vorkosigan House when he finds a collection of Cetagandan scalps that had been presented to his grandfather Count Piotr by his guerilla followers during the Cetagandan war. Miles says he doesn't know what to do with them (the option of throwing them away probably would have been perceived as a gratuitous insult to the Dendarii hillmen's loyalty), and muses that The Emperor might use them as a Take That to Cetagandan diplomats but otherwise they would just have to stay in the attic.
The Alternate History novel Resurrection Day by Brendan DuBois takes place in a United States where the Cuban Missile Crisis turned into World War III. The US is a military dictatorship ruled by General Ramsey "Rammer" Curtis. While looking around his house, the protagonist is disgusted to find a melted brick from Moscow's Red Square, embedded in several inches of glass with radiation warning signs.
In "The Golden Spinning Wheel" from A Bouquet of Czech Folktales, the heroine's wicked step-mother and her step-sister murder the poor girl and keep her legs, arms and eyes. The step-sister looks just like the heroine and takes her place as a nobleman's bride. They later trade the human remains for parts of a precious golden spinning wheel.
Dexter keeps blood sample slides of all his victim in his apartment, hidden in a box in his air conditioner. In the books, he keeps them on his bookshelf. The idea is that, as a serial killer, he can't stop himself from taking a trophy, and the tiny, easy-to-hide, easy-to-get-rid-of slides are a pretty good idea. Even in their "convenient to hide" form, the trophy box bites him in the ass when Doakes finds it... In season 7, when his sister Debra finds out about him, he decides to get rid of them.
The Ice Truck Killer from season 1 was killing prostitutes. He exsanguinated their bodies and staged their chopped up body parts to taunt the police. He stored the blood in the freezer, but it was later subverted — he used it for another staged crime scene.
In season 3, Miguel Prado tries to take a ring from his victims, and he takes one from Ellen Woolf.
The Trinity Killer from season 4 kept plaques from various places all over the USA on the wall in his living room. They marked houses he built for a charity organization, but also each cycle of his murders. Also, a small boy was buried in the concrete foundations of the houses. He was sending postcards to his daughter from those places as well.
The rape gang members from season 5 apparently indulge in this trope. Boyd, the killer of the women and the last link in the chain, keeps numbered strands of their blonde hair. Another member took a piece of their jewellery. They made videos of torturing and raping them, and kept the numbered CDs, and finally, their leader Jordan Chase has a vial with blood of their first victim and wears it around his neck as a pendant.
A serial killer nicknamed Tooth Fairy from season 6 has a tin box with his victims' teeth.
Louis Greene, a wannabe serial killer (or just a really weird guy) acquires the prosthetic hand that belonged to the Ice Truck Killer.
Speltzer from season 7 was a very disturbing serial killer who would persuade young women to come to see him... to houses and buildings he tailor-made as mazes to chase them there while wearing a creepy Minotaur-like mask. When he killed them, he took their earring and put it on display in a mausoleum in a local cemetery.
In the season 8 finale episode of New Tricks "Tiger Tiger", the team discover that their victim was the first victim of a Serial Killer, who collected parts from his victims and stored them in old VHS tape boxes. To add to the creepiness factor, the bad guy kept the body parts in Punny Named video cassette boxes too. The fingers were kept in a box marked "Goldfinger".
The unnamed hitman in "Battleground" (adapted from the short story by Stephen King) collects trophies from his victims, usually a personal item from their room. When he murders a toymaker, it's implied that this habit enables his witch mother to track the hitman to his apartment.
From Angel: Connor, upon returning to Earth from a hell dimension, carries around bits and pieces of demons he's killed. At one point, after a fist fight with a drug dealer, he cuts the guy's ear off to add to his collection.
Ronon Dex of Stargate Atlantis has the handle of his faithful Ray Gun wrapped in Wraith hair. A Deleted Scene also has him showing Carter a necklace made from the fingerbones of Wraith he killed.
A mutant serial killer who appeared in "Squeeze" and "Tooms" took small trophies from his victims, e.g. a coffee mug, an ornamental snowstorm globe or a hairbrush. Agents Mulder and Scully find this kitschy collection in his apartment.
"Our Town": The town of cannibals kept victims' heads in a cabinet. They were found at Mr Chaco's, but the whole town was guilty.
"Paper Hearts": John Lee Roche was a serial killer who murdered sixteen little girls. He cut a piece of fabric in the shape of a heart from their clothes. He placed the cloth hearts in a copy of Alice in Wonderland and kept the book in his car, thus being the 'carrying the trophies by himself' variety.
Firefly: It was said about Reavers that they skinned people alive, raped them repeatedly, ate their flesh and then murdered them. They kept the skins as trophies and their spaceships were covered with blood. They even tied whole corpses to the front of their ships. Mal used this piece of knowledge to trick them while Dressing as the Enemy in the Big Damn Movie, giving Shepherd Book the "honour" of being centre on Serenity's nose. They later gave him a proper burial on Mr. Universe's planet.
Subverted in one episode of Murdoch Mysteries. A suspect was seen talking with a victim on a train and he admitted he liked her a lot. They found he has home-made jewellery made of human hair of multiple people, and the victim's hair is among them. However, she gave it to him voluntarily while she was alive. Jewellery from human hair was still seen as very weird, but he was not her murderer.
Comes up a few times in Hannibal, where it's noted that a common part of Serial Killer pathology is collecting trophies from their victims.
The presence of human remains in home-made fishing lures — specifically, bits of tissue, bone and hair from the known victims of a serial murderer — is the smoking gun which convinces the Behavioral Sciences team that Will Graham is an active serial killer. It's a frame-up, and by the time Graham is seemingly exposed as a killer, the audience knows who's really responsible.
I hold your hand in mine, dear, / I press it to my lips. I take a healthy bite from / Your dainty fingertips. My joy would be complete, dear, / If you were only here, But still I keep your hand as / A precious souvenir. The night you died I cut it off. / I really don't know why. For now each time I kiss it / I get bloodstains on my tie. I'm sorry now I killed you, / For our love was something fine, Until they come to get me / I shall hold your hand in mine.
Champions of Khorne collect skulls from their victims. These are usually piled up in some sort of a shrine, though many a champion carries a couple of favourites with himself, often by skewering them on some Spikes of Villainy.
Many warriors from Warhammer. The most prominent among those are Gorthor, who wears a fur cloak made of the skins of beastmen shamans he killed (showing his badassitude, as well as his belief that gods are with him - he can freely kill a shaman and suffer no curse for it), and the ratmen warlord Queek headtaker who, showing courage unharacteristic for his race, loves single combat and goes to battle with an actual trophy rack on his back.
Inverted for the Slaaneshi champion Lucius the Eternal in Warhammer 40000. Lucius is blessed with an ability to "always triumph" — allowing him to reincarnate in the body of his killer, as long as they feel at least a bit of satisfaction over the deed, fusing them into his suit in the process. So every screaming face on his armor is someone who managed to beat him in the past.
Dungeons & Dragons module G1 Steading of the Hill Giant Chief. One chest has some dwarf and elf ears, presumably taken from victims the giants killed.
In Legend of the Five Rings, there is an ogre who fancies himself a sort of a samurai — his symbol is a collection of mons from samurai he killed, stitched together.
In the Meet the Medic video for Team Fortress 2, the Medic is revealed to be keeping the living head of a Blu Spy in his refrigerator. He also has several still-beating hearts in there.
League of Legends champion Rengar uses this as a game mechanic. He can purchase an item called the Bonetooth Necklace that gives him trophies on a kill or assist. The necklace gives various bonuses depending on how many trophies he's stacked up. More explicitly morbid is the ultimate upgrade it can recieve, the Head of Kha'Zix.
In Grim Fandango, Hector LeMans owns a greenhouse surrounded by a seemingly endless field of flowers. That by itself doesn't sound bad... except in this game plants are a symbol of death within death, and all of that green beauty is actually the remains of people who have been killed by Hector over many years.
Manny: (looking at the water tanks outside the greenhouse) Hector supplies water to keep the flowers alive? Does he see them as a memorial, or as trophies?
It's hard not to get this vibe off some of the costume outfits in Fallout: New Vegas and Fallout 3. Raider sadist armor has a pair of severed hands hanging off the hip, and the Merc adventurer outfit has a necklace of teeth.
In the Adventure mode of the game, humanoid bosses often wear creepy items like "elf bone earring" or "human nail crown". It is not mentioned directly, but, with the extensive killings lists and overall badassery of the owners, the game strongly implies that these items are made from the remains of their previously slain enemies.
There's one player who modded in genitals for humanoids so he could have his character cut them off his kills and carry them around in a sack, and then he started using the sack as a weapon. Thankfully, at some point he had a moment of clarity and asked himself, "What the fuck am I doing?!" and deleted the save file.
Somehow done unintentionally in the Pac-Man and the Ghostly AdventuresLicensed Game — Pac collects the eyeballs of the ghosts he defeats. The dialogue introducing this mechanic briefly lampshades its strangeness, but it ends up painting Pac as a deranged serial killer of some kind.
Roy Greenhilt initially wanted to wear Xykon's teeth as a necklace in case of a victory, but after the lich was blown to bits, he settled on Xykon's crown.
Gannji the lizardfolk mentions that keeping a Creepy Souvenir is common amongst ogres. So, when his friend Enor (an ogre/blue dragon hybrid) is forced to kill him, Gannji suggest he keep his tail as trophy in order to resurrect him later.
In The Greatest Gift, Astra and Mars find a locked box formally owned by the second Big Bad, Venus (actually Jupiter, Astra/Venus' twin sister who stole her name) who's a Serial Killer. The contents aren't as bloody as one would expect, but none the less creepy, not to mention traumatic for Astra. The contents are the severed head of Astra's doll (which Jupiter beheaded just for spite), a piece of the tea pot she used to permanently scar Astra's head, and (most befitting of this trope) the rope Jupiter used to strangle their mother to death while Astra was Forced to Watch. As if we needed another reminder that Venus was a psychopath.
In Homestuck, after Tavros' atrophied legs are sawed off, Vriska decides to keep them. She wasn't the one who sawed them off. She was responsible for the incident that left Tavros crippled and unable to walk, but that's another story. And after Tavros' death, Gamzee cuts off his head and makes out with it. That boy just can't catch a break, can he?
SF Debris: A review of "Winter Is Coming" from Game of Thrones has a hilarious In-UniverseDrinking Game: take a shot for every severed head and for every naked girl. One head fallen off was presented as this trope: "Here's a souvenir for some lucky fan!"
In one episode of Teen Titans, a robot named Atlas kidnapped Beast Boy, Starfire, Raven, and Cyborg and challenged Cyborg to a match and said that he would keep the other Titans as trophies if Cyborg lost. Thankfully, Cyborg won.
In one episode of SpongeBob SquarePants, Spongebob and Patrick accidentally unfreeze Manray, who was Mermaidman and Barnicleboy's worst enemy, kept in frozen tartar sauce as a souvenir.
In an episode of American Dad!, we learn that Bullock likes to collect human fingers, a habbit he claims he started when he was in Vietnam. He then explains that he was only in Vietnam a few years ago.
An episode of Star Wars: The Clone Wars had a clone who collected droid fingers from battles. In-universe, it was considered contraband and downright creepy.