This happens to the protagonist, his girlfriend, his grandfather, and apparently half of Texas.
Also if you listen to the radio they have also done this to Garland, Texas, and if you look around they are planing on doing this to New York City. They already got a school bus filled with kids, you watch them take an airplane, and they have abducted other human-like people from different planets. Plus with a ship that size who knows what else could be up there?
The protagonist of the sequel is one of the passengers on that airliner. He has a few missing years in his memory (starting with the abduction) and is looking for the truth, while working as a bounty hunter on an alien world.
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.
This is also a major component in the reboot. 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.
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.
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.
Super Mario Land, where Mario had to save Princess Daisy (who made 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.
Mass Effect 2 has mass alien abduction; the Collectors are abducting entire human colonies at once. They're using said colonists to build a Reaper.
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 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.
onEscapee is about a man who survives his abductors' shipwreck, leaving him stranded on a distant planet.
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.
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.
EarthBound Beginnings uses this twice. 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. And 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.
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.