Maburaho has a collector as a full-time character after her introduction. Her stated goal is to make a certain ghost a part of her collection.
Yu-Gi-Oh! GX has a minor character named Giese Hunt, a self-stylized Duel Spirit hunter after Johan's prized (and - until Episode 130, nonexistent) Rainbow Dragon Duel Spirit to add to his collection of trophies, even capturing his Sapphire Pegasus Duel Spirit as bait. Not surprisingly, this fixation stemmed from a childhood trauma where he was the victim of Duel Spirit theft.
In the second Pokémon movie, the villain targets the three legendary birds Articuno, Zapdos and Moltres in order to force the legendary Lugia out of hiding, so he could have them all in his collection. Of course, the real problem for the heroes wasn't just that he was merely collecting, it was that his attempt disturbed the balance between the three birds which lead to global weather chaos.
The movies soundtrack even gave us the official collector Villain Song "Ware wa collector" (I am a collector).
Mikogami Hayato from Sekirei, who aggressively pursues any Sekirei that catches his fancy in an effort to grow his collection. His behavior is very much like a Pokemon master, even declaring that he wants one because it's a rare fire-type!
The Marvel Universe has an Elder of the Universe known as The Collector, whose mania for collecting is so strong it makes him immortal. (Or maybe he took up collecting to keep himself from going mad because he was immortal. After doing it for billions of years, it's often hard for even him to remember.)
Kate ran into one of these in Hellboy while trying to find an alchemical guide that would let them rebuild Roger the Homunculus. He would only give it to them if Abe became his prisoner. Kate ended up freeing the demon The Collector had enslaved and it killed him.
Tom Strong was once captured and imprisoned in a comic book with other "science-heroes" by Horatio Hogg, Collector of Champions.
In Sillage #2, Enshu Atsukau wants to add Nävis to his "collection".
While Brainiac's origins vary, his goal is always to collect a piece of every civilization on all worlds, then destroy the rest of that civilization.
In one Garfield strip, Jon finds a box that Garfield is saving:
Jon: It's full of mailman hats!
Garfield(grinning) I'm collecting them.
Jon: What happened to the mailmen?
Garfield(surprised) They've escaped!!
Toy Story 2 is about Woody getting "kidnapped" by a collector who wants to sell him to a museum in Japan. Woody is actually a toy, though.
Buzz Lightyear of Star Command, "A Zoo Out There" features the Chlorms, who regard every other species as "lesser beings", kidnapping members of the Galactic Senate (and eventually Team Lightyear) to put in their zoo.
Done in the ×××HOLiC film, "A Midsummer Night's Dream" when Yuuko gets an invitation stating that her 'collection' is not complete. She brings Watanuki and Doumeki along with her into a mansion where there are several other collectors that collect rare things. It later turns out that the person that invited them there is a collector that collects collectors who collect unusual things. He keeps both their souls and their collections in individual rooms. He started because someone who was close to him collected something, and asked him to start a collection too.
John Fowles' 1963 novel The Collector features a psychologically unstable butterfly collector 'collecting' a young woman he has seen around town, and keeping her in his cellar. It was also adapted into a film.
The Trafalmadorians in Slaughterhouse-Five kidnap the main character, take him to their planet, and display him in a zoo. Lessons about free will and predestination are learned.
In the Nightside novels by Simon R. Green there is a character who is called "The Collector." He has unique items from the past, the future, and alternate time-lines. He is also fairly paranoid about other collectors stealing from his collection. He once went so far as to store his collection on the Moon. Didn't stop JohnTaylor from accessing it, though.
Doctor Who has a variation on this in "The Space Museum".
It also turns up in the Expanded Universe novel "The Last Dodo" featuring a museum dedicated to endangered species throughout the universe with a curator quite interested in a certain Last of His Kind Time Lord.
An example from the new series turns turns up in the Ninth Doctor episode Dalek, where the eponymous Dalek is the prize specimen in Henry van Statten's museum of alien artefacts. Upon realizing what the Doctor is, van Statten tries to collect him too.
The Twilight Zone had a newlywed couple wake up in a small, deserted town, only to find out at the end that they were toys in a giant alien's playset.
"People Are Alike All Over" ends with apprehensive astronaut Conrad finding that the house the seemingly-kind aliens have built for him is actually a cage in a zoo exhibit.
Star Trek: The Next Generation, "The Most Toys": Data is kidnapped by Kivas Fajo to add to his collection of unique objects. At the time, everyone (including Data) thought that Lore, the only other sentient android in the known world, was dead.
Criminal Minds Fisher King two-episode story uses the trope-naming book as an important story key. the UnSub is almost like the psychotic protagonist of the book.
The show makes use of the "collector" subtype of serial killer later on in "The Uncanny Valley," with a damaged woman who puts other women in a state of chemically-induced paralysis and makes them up as dolls.
In the Masters Of Horror episode "Cigarette Burns", the millionaire collector Bellinger collects various films depicting extreme acts. He's also keeping a mutilated angelic creature locked up in his gallery as part of his collection of La Fin Absolue du Monde.
The vampire Luthor Harkon in Warhammer Fantasy Battles collects dead sailors (as zombie pirates in his fleet) and Mayincatec artefacts in a hope to get his magical powers back and is also utterly insane.
A lot of medusas have done this too, but many in later editions are much smarter, avoiding keeping the petrified remains of their victims as trophies; if potential victims come into their lairs and see such things, what's the first assumption they're going to make about who the lair belongs to?
Trazyn the Infinite, a Necron Overlord in Warhammer 40,000, has this as his particular quirk, and has a whole planet dedicated to his obsession. Artefacts of note include the preserved head of Sebastian Thor (Which then begs the question what happened to the body), the husk of an Enslaver, and a giant man clad in barqoue power armour whose face is locked forever in a tormented scream. It's partially for his own amusement, and mostly because he wants to save important pieces of history.
The main antagonist from LittleBigPlanet, appropriately named The Collector, goes around the various levels kidnapping major characters in the background.
The entire plot of Mass Effect 2 revolves around fighting an enemy known as the "Collectors," who are named for their tendency to "collect" samples of unusual and unique biological specimens for genetic experiments. They are abducting human colonies, are actually working with the true villains of the series, the Reapers, and are repurposed Protheans from the last time the Reapers invaded. In the end Shepard's own crew is abducted, and the final part of his/her mission is a rescue op to bring them back. Unlike many of the other examples on this page, their goal is not to display their victims, but to dissolve them into their genetic components and build a new Reaper from human goo.
Cyrille Le Paradox, the Big Bad in Sly Cooper: Thieves In Time. He is introduced as a wealthy museum owner who collects historical artifacts via time travel and plans to steal the Cooper clan's canes throughout history to form his own collection to achieve revenge on them.
ˇMucha Lucha!, "The Collector" features an alien trying to collect masked wrestlers.
In the Superman animated series, the two-parter "The Main Man" featured both Superman, the last surviving Kryptonian, and Lobo, the last surviving Czarnian, being captured by an alien called The Preserver, who kept a menagerie of such creatures (he even had a dodo among them).
And you have to include Brainiac, who ensures that his collected data is one of a kind by destroying the planet he got it from.
In 2007, an alien villain named The Auctioneer captured Supes and several dozen other heroes. Guess what he planned to do with them?
Parodied in a Halloween episode of The Simpsons, wherein the Comic Book Guy kidnaps his favorite celebrities, including Tom Baker, Matt Groening, and Lucy Lawless, and encases them in mylar bags.
Powerpuff Girls, the episode "Collect Her" finds our titular heroines being captured by Lenny Baxter, a comic book geek who has collected every piece of Powerpuff Girls merchandise in existence and, desperate for more, has decided to add the Girls themselves to his collection. He is defeated when the townsfolk track him down and torture their whereabouts out of him by removing his valuable toys from the boxes.
In the Chip 'n Dale Rescue Rangers episode "Three Men And A Booby" — stop that snickering, unless it's because of the Three Men And A Baby reference — an obsessed egg collector collects a booby egg. The mother booby enlists the Rangers' help in reuniting the egg with her. They end up hatching his entire collection.
D.N. Amy from Kim Possible eventually makes Rufus and Steve Barkin into one giant living cuddlebuddie for her collection.
One villain from Bonkers, a toon that collected other toons, was actually called "The Collector". Only it turns out he wasn't actually a toon. He was a crazy human who thought he was a toon. He remained in denial even after his mask was torn off, screaming "I'm a toon! I'm a toon!". It was incredibly creepy.
In the Sushi Pack episode "Collect 'Em All," The Collector captures the Sushi Pack to add to his collection, but gives them one chance to win their freedom in a remote controlled car race.
In what may be the strangest example ever, Ringo Starr from the cartoon The Beatles. In the episode "Ticket to Ride", the others are revealing their hobbies (painting, science, etc.), and it turns out that Ringo likes to kidnap women and put them in bird cages ("bird" being Liverpool slang for "girl"). Fortunately, he's really bad at it; he's only managed to trap one girl, and she escapes during the course of the episode.