Washington Irving's The Legend of Sleepy Hollow: The story isn't even 30 pages long, and Ichabod's entire encounter with the Headless Horseman only lasts 1 and a half pages—but it's also the most memorable part of the whole tale.
Steven Erikson's Malazan Book of the Fallen has several underused-and-awesome characters. One of the more notable examples is Hood, the god of death.
How awesome is he? The first time Hood actually does anything personally, he pushes Chaos several leagues back from the wagon in Draginpur, just by showing up. The next time, he rips the face off of a Forkrul Assail Pure. With his teeth. And then, he tears another one apart with his bare hands.
There is usually at least one scene in every Discworld book featuring Death (The Wee Free Men is one of the few books where he doesn't appear). Except in the book where he stars, these definitely count.
Oberyn Martell quickly gained a legion of fans during his limited time in the series with his many witticisms and exotic background story. He continues to appear in flashbacks, perhaps as a result of this trope.
Syrio Forel is also quite popular despite his limited time in the series, to the point that some fans still claim that he might still be alive, despite all signs pointing to the contrary. Just so.
Archmaester Marwyn shows up in one scene (though he is mentioned a few times previously) to drop the bombshell that the maesters had a hand in the Targaryen dragons dying out, then he promptly hops on a ship heading east, to join up with Daenerys.
Septon Meribald and the Elder Brother are bit characters, muggles, unconnected to any of the major figures, yet their speeches about War Is Hell is widely considered to be among the emotional highlights, and some of the best writing, of the entire franchise.
Cortnay Penrose's only scene was also pretty awesome.
Wylla Manderly's only scene gained her legions of fans for calling out the Freys on their bullshit, and sticking up for the Starks when no-one else would.
Older Than Print: Mi Heng only appears in one chapter of the 2000+ page Romance of the Three Kingdoms, but is still one of the most memorable characters for his sheer balls in insulting every single person he meets, no matter how powerful they are. He ends up throwing out insults until the second his head is cut off.
In Bruce Sterling's Schismatrix, Nikolai Leng's Mechanist wife shows up in three of the tiny (around ten lines each) chapters of Twenty Evocations, a short story included in later editions.
In the original book version of The Wonderful Wizard of Oz, the Wicked Witch of the West appears in only one chapter. Nonetheless, that one chapter led to her becoming one of the most iconic villains in film history.
Merlin in The Warlord Chronicles. Doesn't have a lot of time directly interacting with the protagonist in the story, but every bit where he is doing so, it's damn memorable.
Irene Adler only appears in one of Arthur Conan Doyle's Sherlock Holmes stories, but is considered almost as essential a character to include in adaptations as Holmes and Watson. Moriarty is also the quintessential nemesis for Holmes, despite only appearing in two stories.
Technically, Moriarty never appears in the stories, since Watson never actually sees him (except possibly once through a train's window). All that Watson knows about Moriarty is what Holmes has told him in passing.
Laurent in the Twilight saga had a considerable following in the early years of the fandom, even though he appeared only briefly in the first two novels. There was a ridiculous internet backdraft when the "olive" skinned French Laurent was portrayed by a black guy who was most definitely not French.
Tom Bombadil in J.R.R. Tolkien's The Lord of the Rings. He enters the story for a brief and memorable episode and is then never seen again.
In The Dresden Files novel Small Favor, Eldest Gruff at the very end of the book. He teleports in, stomps around the island and shaking the earth with every step, one-shots a Fallen Angel, chats up Harry, and then goes to get a donut.
In Changes there's Donnar Vadderung, otherwise known as Odin. He gets a single chapter with dialogue and briefly appears at the end but he effectively comes off as a divine David Xanatos.
Ferrovax the dragon appears briefly at a party Grave Peril, stamps Harry Dresden into the ground with the sound of his voice, and is never seen again. He's implied to be one of the most powerful beings alive.
Percy Jackson and the Olympians Artemis. The god with the fewest book appearances... no children and least divine lackeys... and guess who is one of the most popular gods on Fanfiction.net? (Until her brother Apollo got his own spin-off series, he counted as well.)
From The Heroes of Olympus we have Tartarus. Not just the realm, the actual protogenoi himself. Percy and Annabeth spend the entirety of The House of Hades on a grueling trek through the deepest and darkest pit in the Underworld, all while fending off the most horrible monsters along the way. Then for the first time ever he creates his own horrifying physical form, just to deal with them in person. He's so terrifying that firmly established badass Percy nearly shits a brick.
Marek Oramus's Polish sci-fi novel Senni Zwyciezcy has a very brief scene where a character buys a talking can of beer which encourages her to drink it. This became the most famous scene in the novel—to the point where a 1989 edition is illustrated with the image of a beer can, and the back-cover blurb quotes that scene.