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.
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 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 Lord of the Rings. He enters the story for a brief and memorable episode and is then never seen again.
In Warrior Cats, Mapleshade has all of three scenes during her first appearance, and one in her second. She does nothing important, but fans still remember her for her epic and creepy lines and trying to drown Ivypool all while reminding Ivypool of Daisy.
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 Apollo and Artemis. Two gods with the fewest book appearances... least important children slash divine lackeys... and guess who are the most popular gods on Fanfiction.net?