Dreamworks' promotional posters do this ALL. THE. TIME. Actually, this applies to a lot of animated companies. The difference, of course, is that Disney, for example, generally limits it to an in-film expression unless it practically defines the character (there's a reason why Buzz Lightyear wears it on his poster and Princess Ariel doesn't, even though they both do it within their films).
The Killer Dame by Odon. Tuvok and Seven of Nine, both skilled practitioners of the Fascinating Eyebrow, use this as a means of communication when they're tied up by Hirogen captors.
The young Borg realised that Tuvok was enquiring if she was all right. Seven quirked her ocular implant in reply, conveying that such a question was irrelevant and she was currently trying to free her bonds. Tuvok raised his other eyebrow, conveying his disapproval at the emotion of arrogance that might distract one from the task at hand. Seven answered with a scowl, conveying that she was experiencing some difficulty with the knots but she was Borg and would adapt, and that she would be as arrogant as she wished thank you! Tuvok took a deep breath, dropped his eyebrows to normal level, then raised first the right brow, then the left brow, then both brows together, then the left, then the right brow, two raises of the left again, then a wiggle of his pointed ears, then a slight twitch of his right brow again, and last of all a final poetic dance of supercilium motion by the two hairy arches.
Jake Blues' right eyebrow seemed fixed in this position.
Vetinari of Discworld fame often used the Fascinating Eyebrow along with a finishing blow in a verbal power struggle to make sure the opponent knows he's been defeated. (This is highlighted in Making Money, wherein Cosmo Lavish, one of the antagonists, actually practices raising one eyebrow in front of a mirror in an attempt to emulate the Patrician.)
What's worse, Cosmo couldn't actually raise his eyebrow on his own. He has to rely on a small mechanical device to raise his eyebrow for him.
There is a small asylum dedicated to people who think they are Vetinari. They have eyebrow-raising competitions.
The protagonist of Are You There God? It's Me, Margaret. can raise one eyebrow and does it occasionally to get adults to stop asking her questions. She doesn't know why it has that effect, but it does.
The Queen's Thief LOVES this trope. Not only is the main character a master of this art, so is his love interest.
Elizabeth Bennet of Pride and Prejudice has a fascinating eyebrow that has a tendency to rise when she comes across things she finds particularly ridiculous or wryly amusing. It's one of the many pride things going on.
In Chrome Circle by Mercedes Lackey and Larry Dixon, Tannim's mentor, a dragon currently wearing human form, arrived (magically) in response to a call for aid and "raised one long eyebrow at Tannim in a gesture that Tannim knew perfectly well had been copied after long study of Leonard Nimoy."
In The Mortal Instruments Clary is annoyed when Jace does this at her, because it is an ability she has always envied. She gets even more annoyed when Magnus Bane turns out to be able to do it too.
During Galaxy of Fear a rather absurd suggestion is made, and Hoole raises an eyebrow. Tash thinks that "it was as close as her stone-faced uncle would ever get to looking surprised."
In "Royal Flash" Flashman has to impersonate a royal who has this Character Tic, and is driven to strange facial twitching while trying to rehearse it. Eventually the conspirators give up and just hope no-one notices his eyebrows go up in unison.
Supernatural has the Trickster/archangel Gabriel do this a lot just before he dumps the Winchesters into something particularly nasty (possibly because Richard Speight Jr, who plays him, has the amazing habit of doing it.)
Angus Deayton's eyebrow soon gained a fan following in its own right on Have I Got News for You. Paul Merton mocked it a lot.
Spock (the Trope Namer) popularized the Fascinating Eyebrow amongst Star Trek fans, though it rarely denoted amusement. Such an emotional response would be... illogical. According to Kirk, it "usually connoted some combination of surprise, disbelief, and/or annoyance".
And another Expanded Universe novel involved Sulu, Chekov, and a random engineer doing an impression of a typical Kirk/Spock/McCoy interaction, complete with Chekov attempting and failing to raise one eyebrow.
The Doctor from the same series was a master of it.
Data from TNG, although being an emotionless android, had his share of Fascinating Eyebrow moments.
Captain Picard also did this a few times. In his Nitpicker's Guide series author Phil Farrand jokes that this is a result of his mind-meld with Spock's father Sarek. Vulcans all over Trek are masters at the Fascinating Eyebrow.
In the novel Well of Souls, Talma Pren (a Human) canít do it, but Vaavek (a Vulcan) can. Talma muses that all Vulcans seem capable of doing so.
Stargate SG-1: Teal'c and the eyebrow are virtually legendary, typically whenever he learns about a new bit of Tau'ri oddity, often accompanied by him saying "Indeed."
The hundredth episode special featured a Show Within a Show version of Teal'c whose actor (or rather the fake actor playing the fake Teal'c on Wormhole X-treme and being played by a real actor on SG-1) apparently couldn't pull off the Eyebrow. There's a shot of him being assisted by a piece of string taped to his face.
Sylar, especially since Zachary Quinto's eyebrows are so prominent. In the episode "Five Years Gone," when Sylar is using an illusion to disguise himself as Nathan Petrelli, who is president, Zach recorded Nathan's lines so that Adrian Pasdar would know how to say them, but the episode got to a point where Sylar!Nathan cocks his head to the side and stares at Mohinder, but it didn't look right because this trope was missing, since Adrian Pasdar can't cock his eyebrow like that.
Of course, ZQ's ability to do this came in handy when he was cast as Spock in the Star Trek reboot.
When Lucius Vorenus of Rome does this, you KNOW something is about to go down.
Fascinating Eyebrow is one of Agent Scully's trademarks. She would usually eye down Mulder for his crazy theories. It was known among fans simply as "the look".
The Stupendous Yappi who appeared most prominently in "Clyde Bruckman's Final Repose" is a Phony Psychic or Not-So-Phony Psychic; which one depends really on your interpretation. His eyebrow raise might be considered Exaggerated version. Interestingly, his look was intended to Agent Mulder who for once did not buy his seer routine and thought him a fake.
Earl from My Name Is Earl usually does this when going into thoughts, usually followed by Earl narrating what he did next in that episode. It is actually referred to by characters on the show some times.
Angel. In "That Vision Thing", Angel has to free someone from a prison dimension, which turns out to be guarded by a ferocious-looking yet amiable demon called Skip. Before they start giving each other the Nothing Personal speech followed by a No-Holds-Barred Beatdown, the two share some amusing eyebrow movements as they wordlessly assess each other.
Part and parcel with the more dynamic and emotive designs of Transformers Animated, and not just the humans, either. Ratchet has some excellent ones when trying to understand the younger members of the team, and even Prowl with his highway patrol shades gets in one or two Fascinating Optic Ridge moments, to humorous effect.
In Transformers Prime, with the somewhat more emotive movie based altmodes, Optimus Prime does this, when Miko and Raf lie to him about Bots being involved in street racing.
Used one time by a car dealer on Futurama upon Amy mentioning how rich her parents were. He had to physically restrain it.
In Superman/Batman: Public Enemies, Lex Luthor did quite an impressive version of this when Power Girl walked into his office with "something to talk about." Given that Power Girl, is, erm, powerful even by DC's standards, one can't help but be suspicious of his intentions.
In Fireman Sam, Station Master Steele's face appears to be stuck this way.
Princess Celestia does this near the end of "Lesson Zero", as Twilight's friends are taking the blame for her casting a spell that makes the entire town fight over a doll so that she could learn some sort of lesson about friendship to send her for that week.
Octavia, one of the many fan-favourite background characters, pulls this expression in "The Best Night Ever" when Pinkie makes a request. Even her wiki page uses it.