In Baldur's Gate III, the mind flayer that captures you in the intro has Combat Tentacles on its nautiloid that teleport people they strike into tanks on the ship for later infestation with an illithid tadpole.
In Bully, after Jimmy Hopkins collects all the radio transistors for The Hobo, the latter is beamed up into the sky, implying that he was voluntarily picked up by a UFO.
Caveman Warriors: The story mode starts with an alien spaceship grabbing a couple cave kids with robot arms.
One mission in Destroy All Humans! involves abducting a beauty pageant winner. Several side missions also require you to throw a number of people or cows into the Mothership's Abduct-O-Beam.
Nearly every adult resident of Youngtown was abducted by aliens at some point before the protagonists arrive there, leaving it to become a Never Land populated almost entirely by children.
In the game's Back Story, the protagonist's great-grandmother and great-grandfather, Maria and George, were abducted and held for an unspecified amount of time by a Sufficiently Advanced Alien race. Maria became the surrogate mother of the then-infant Big Bad Giegue and raised him to adulthood, while George studied and presumably gained the ability to use PSI, well against the alien race in question's wishes. George eventually made it back to Earth, but Maria wasn't so lucky.
Echoes: Operation Stranglehold: The Hybrid Pantheon have managed to capture almost the entire human race, save for about half a million people.
The Fallout 3 add-on Mothership Zeta has the player and various wastelanders being abducted and studied aboard an alien ship. The evidence on the ship indicates that they have been doing this for centuries. In fact, one of the abductees is a Japanese samurai in full armor who proceeds to slice up his abductors with his katana. Naturally, you can't understand each other. Another is a Wild West cowboy, whose Colt comes in handy.
There is a funny cheat mode in FIFA Soccer 2000, which enables a spaceship hovering above the pitch during a match and beaming up players who accidentally happen to stand right under the ship's tractor beam.
In The Legend of Zelda: Majora's Mask, one of the side quests involves some aliens attacking Romani Ranch on the Night of the First Day. They mostly seem interested in the cows, but if Link fails to stop them, they'll abduct poor Romani as well (she was in the barn, trying to save the cows). If she's taken, she'll be dropped back around the afternoon of the Second Day, dazed and having obviously had her mind wiped.
The plot revolves around mysterious aliens called "Collectors" abducting entire human colonies at once. They're using said colonists to build a Reaper.
In the fourth game, Metal Gear Solid 2: Sons of Liberty, the Colonel, shortly after Raiden manages to escape Arsenal Gear's torture room, suddenly starts telling what seems to be a typical UFO story where it is implied that he was abducted while trying to get home from work, giving the early implication that the Colonel is not who, or rather, what, he claims to be.
The third game, Metal Gear Solid 3: Snake Eater, has Sigint remarking that Zero claimed that he was abducted by Aliens once as a reason for him to suspend disbelief in regards to Snake procuring the Spirit Camo.
In the novel within a video game, The Shocking Conspiracy on Shadow Moses, the main character once thought he was abducted by aliens.
Metal Gear Solid: Peace Walker implies that most of the UFO encounters, Alien abductions, and Cattle Mutilations were actually caused by the CIA, more specifically their rogue unit: the Peace Sentinels, and their AI weapons.
onEscapee is about a man who survives his abductors' shipwreck, leaving him stranded on a distant planet.
The plot of Otto Matic goes that Brain Aliens from Planet X are abducting humans to turn them into more of themselves, and it's up to the eponymous Space Police robot to stop them. In each level there are civilians which — once you're close — you must rush to teleport them to safety before a Flying Saucer arrives to scoop them up.
In Phantasy Star Online 2, undertaking specific quests on Very Hard difficulty or above has a small chance of the players' campship getting abducted and thrown into the Darker Den.
In the Taiwanese video game Richman 4, a game similar to Monopoly, one of the events from the "Chance" spot involved the player being abudct by aliens, which sent the player off the board via a UFO for three rounds, being unable to collect any rents during that preiod.
Seedship: A random event can have your colonists get stolen by aliens.
The Simpsons Game Kang and Codos's mooks raid the Springfield mall and abduct people. After Cletus complains that he spend all day cutting out coupons for a new flat screen TV they get impressed by his tiny pieces of paper and decide that they must study him.
The Sims games allow your Sims to get abducted by aliens if they spend too long stargazing. (It's a very small chance without hacks or cheats.) In The Sims 2, they can also come back pregnant with an alien baby... if they're male. Now that's extreme Anal Probing. Even if they're not pregnant, there's a possibility of them starving to death after their return if they aren't fed immediately; the aliens don't have human food, it seems. This was also introduced in The Sims 3: Seasons expansion pack and The Sims 4: Get to Work expansion pack.
In Stellaris, empires that engage in "Active Observation" of a pre-FTL species will abduct specimens for study. Fanatic Xenophile empires won't tolerate the practice and it has a chance of making the natives more Xenophobic.
In Super Mario Land, Mario has to save Princess Daisy (who makes her debut here) from an evil alien who kidnapped her just so he can distract Mario while the game's real villain, Wario can succeed in his evil plans as revealed in the sequel.
Super Mario Galaxy: Rosalina, according to her backstory was actually abducted by the Lumas because one of them thought that she was its mother. When Rosalina realizes that her real family is now long dead since her departure, she eventually becomes their leader, and even helps Mario save both Peach and the entire Mushroom Galaxy from Bowser, who at the same time did this to Peach.
Warframe: In the "Sands of Inaros" quest, we find out that that the primitive human inhabitants of Mars were preyed upon by "golden spacemen," while Inaros did his best to defend them. Eventually Inaros disappeared, and the people were wiped out. The golden spacemen were most likely the Orokin, a human empire of immortals who, among other horrible things, stole the bodies of children.
In XCOM: Enemy Unknown, the most common mission type are alien abductions occurring in major cities across the world. It's also the most straightforward mission type: Kill all aliens on the ground. However, the aliens will always attack three cities on three different continents at the same time, forcing the player to make a choice, as each mission provides a different reward (all of them useful for different reasons), and panic increases in the continents you don't save, putting them at risk to stop funding you. Fortunately, every country with a satellite over them at the start of the month will no longer suffer abductions, so they can be minimized and eventually shut out entirely.
In XCOM: Chimera Squad, one of the investigations involves a string of aliens being abducted, but the abductors are also aliens.
in FIFA Soccer 2000, which enables a spaceship hovering above the pitch during a match and beaming up players who accidentally happen to stand right under the ship's tractor beam.