In Angry Lead Skies, Garrett's associate and housemate the Goddamn Parrot gets abducted by "silver elf" aliens, to the detective's considerable delight.
K. A. Applegate's Animorphs features the Skrit Na, a species that seems to be the basis of "The Greys". As an Andalite protagonist explains in their first appearance, the Skrit Na basically go around in their weird, saucer-shaped ships, abduct people from other planets and either do weird experiments on them or put them in zoos on their home planets. Interestingly, nobody knows why, making the Skrit Na the Cloudcuckoolanders of the galaxy. In this particular instance, the plot kicks off when the Andalites board the Skrit Na ship and rescue the two human teenagers whom they abducted, then try to bring them back to Earth.
Area 51: These were actually faked by Majic-12 to keep people in the dark about what's really going on. People abducted are implanted with fake memories which make it appear real.
Andrey Belianin's The Thief of Baghdad: The protagonist (who lives in Ancient Baghdad) is snatched by a Tractor Beam while running away from the sultan's guards. The guards, seeing the hateful thief taken by Saint Hyzr's Chariot, assume he's gone for good. The thief, who is actually a modern-day man transported into the past by a genie, whose spell also caused Laser-Guided Amnesia, breaks away from the short grey aliens and forces them to engage in conversation. They use their telepathy to tell him that they are agents of an interstellar union, made up of various races. They are scouting Earth before announcing their presence and integrating humanity into the galactic community. They claim they wish to eliminate racial, religious, and sexual differences among humans. When the thief hears about the latter, he decides to show the aliens why humans enjoy their sexual differences.
In The Brass Dragon, the protagonist initially can't remember the last year of his life, but unexpectedly finds that he now knows a lot more about mathematics than he used to. He and his alien companions were trapped on Mars for most of that year, since they had to wait for an enemy ship to be available to ambush for transport back to Earth. They passed the time by teaching the protagonist a lot of math.
Hunters Of The Red Moon: Co-written with her brother Paul Edwin Zimmer, this story has the protagonist, who is sailing around the world alone, kidnapped off his boat by the Mekhar (who trade in slaves, and were expecting more people to be on the boat).
Adam R Brown's Alterien: Strange people, Oberon Navarro later learns are aliens, take him from his home and return him completely changed and without any memory of his life.
Bruce Coville's Book of... Aliens II: Happens to George Pinkerton and his friend Billy in George Pinkerton and the Space Waffles (the titular aliens want to question them and find out if Earth is suitable for invading and colonizing), the protagonists in Fine or Superfine (who aren't sure why they've been abducted), and a kid in Hunters (who was abducted to be studied).
In Christopher Buckley's novel Little Green Men, alien abductions are the work of a top-secret U.S. government agency which had been manufacturing evidence of alien activity since 1947, and didn't start doing abductions until UFO sightings, crop harvesting and cattle mutilations had lost their novelty value. The rectal probing and egg harvesting only started because the abductees seemed to demand it. Actual Little Green Men aren't used any more because of the difficulty of obtaining midgets with security clearances.
Discworld: Although no "aliens" have appeared, there are footnotes that poke fun at this trope, remarking that so many aliens seem to hang around isolated backwoods roads, waiting to abduct humans, that they keep screwing up and abducting one another. Actual "abductions" are done by The Fair Folk.
Robert A. Heinlein's The Puppet Masters: The titular aliens have been abducting humans for years, possibly centuries, as part of the plan to conquer Earth. It turns out that the protagonist's Love Interest was abducted from a human colony on Venus as a child; this provides a key to the eventual defeat of the invasion.
Budd Hopkins's Intruders: Features real life narrations of alien abductees's experiences. Mostly jogged and brought to the surface via hypnosis.
Mindwarp: The disappearance of Todd Aldridge is a major background event, and the other kids struggle to avoid his fate.
In Mr Blank, Mina is abducted by aliens. Though in that world, the aliens (referred to as Little Green Men despite being of the modern Grey variety) are one of any number of conspiracies that secretly control the world. Other groups want power, the LGM just want to kidnap and probe.
My Teacher Is an Alien: Susan learns that her new teacher is actually an alien named Broxholm, assigned to abduct the class' smartest, least intelligent, and five most average students to study. She teams up with geeky Peter and bully Duncan to stop him, but Peter leaves with Broxholm willingly. The rest of the series reveals more about the aliens and why they want to study humans in the first place.
Kim Newman's "Angel Down, Sussex": The monster is obviously a by-the-book abductor alien. However, it's also an Empathic Shapeshifter, and the story's set in Edwardian times before such urban legends became widespread. Consequently, different people encounter it as a succubus, one of The Fair Folk, or whatever else the earlier equivalent would have been.
Daniel Pinkwater's Slaves Of Spiegel: Steve Nickelson is abducted by Space Pirates, who have him and everything in his Hoboken restaurant wrapped in aluminum foil, shrunk in size and taken to the planet Spiegel for the pirates' great interplanetary cook-off. Steve sends in a report to the Flying Saucer Club of Hudson County, New Jersey, who pronounce his report to be totally inauthentic since all aliens are either Little Green Men or blobby eye stalk creatures, not "fat people," and nobody has ever heard of a planet named Spiegel. The Space Pirates then find out about Steve's assistant, Norman Bleistift, and kidnap him too.
Tunnels: The Styx, although they come from within the Earth and not from Outer Space, routinely do these to people who discover their secret city and scientists whose knowledge they desire.
Roys Bedoys: Discussed in “Where Are You, Roys Bedoys?”, where Roys stays at Maker’s house for about three hours, and Loys wonders if Roys was kidnapped by aliens.
Kir Bulychev's Half a Life has the crew of an exploration ship find a derelict alien vessel floating in space. Aboard, they find the diary of a woman abducted in 1956 by an automated ship gathering samples of biological life. Since the diary is incomplete, they have to investigate and try to find out what happened to her. She was killed while attempting escape with a group of friendly aliens. The aliens have built a statue in her honor to recognize her sacrifice.
Played With in Wizja Lokalna, where Ijon Tichy is kidnapped by aliens - after he arrives on their planet.
