A Christmas Carol: Averted; a case of Beam Me Up, Scotty! and Memetic Mutation has resulted in "bah, humbug!" becoming the Catchphrase of Ebenezer Scrooge. "Bah, humbug" is only spoken twice in the novel, though "humbug" comes up a few more times by itself. At that time, "humbug" meant "hoax" or "jest", so Scrooge was just dismissing Christmas as a fraud in the lingo of the day.
Sherlock Holmes's Beam Me Up, Scotty! is: "Elementary, my dear Watson", a line never found in the novel series. Then there's "The game's afoot!" which is actually a Shakespeare quote that Holmes utters once in the original stories. He does, however, have at least one genuine catchphrase: "You know my methods. Apply them!" This phrase or variations on it are used maybe six or seven times in the canon, but it hardly ever shows up in adaptations.
Garion's catchphrase in David Eddings's The Belgariad, which the other characters quickly become tired of, is "Why me?" Eventually answered as "Would you have trusted anyone else to do it?", but not before various other characters have taken it up briefly. In one scene Belgarath (who's The Obi-Wan, and usually the one being asked and not answering), says it, much to everyone's amusement.
Silk's is "Trust Me" (which you actually shouldn't) and Errand receives his name because for a while "Errand" is the only word he can say.
A handful of Discworld characters have catchphrases:
Bonus points because this one was also uttered, on request, in "Wizard Language".
Granny Weatherwax: "If you ain't got respect, you ain't got a thing," "I can't be havin' with this," "Blessings be upon this house", and of course written, rather than spoken: I ATEN'T DEAD.
Death: There's no justice. There's just me. Which in Mort became There's no justice. There's just us.
Gurgi mentioned "munchings and crunchings" often enough for them to count as a catchphrase; also his 'Poor Tender Head'.
Fflewdur Fflam used "Great Belin!" as his trademark Unusual Euphemism (Belin is an ancient Welsh sun god),
Princess Eilonwy would often cry "Taran of Caer Dallben, I'm not speaking to you!" or some variation of the same. She also has a habit of talking in similes and metaphors. For example, "It's silly to worry because you can't do something you simply can't do. That's worse than trying to make yourself taller by standing on your head," or "I don't like being called 'a girl' and 'this girl' as if I didn't have a name at all. It's like having your head put in a sack."
In the Mash novels, Hawkeye has "Finest kind!" as a Catchphrase. This made it to the movie, and appeared in some of the earliest episodes of the TV series, but was eventually forgotten or abandoned. Hawkeye and Duke together share the Catchphrase "We're the Pros from Dover".
Characters in Stephen King novels often have catchphrases shared between each other as in-jokes or references to past experience. For example:
Honor Harrington has the phrase 'Let's be about it', which she adopted from her first Captain, and which several of her subordinates have begun using.
In Dan Abnett's Gaunt's Ghosts novels, Beltayn, Gaunt's adjunctant and vox officer, says "Something's awry" to report any kind of problem. Up to and including imminent disaster that could kill them all — a fact Lamp Shaded in the books.
Abnett also uses this with Aemos in Eisenhorn whose favourite phrase is 'Most perturbatory'. It's even his last words.
Kilroy 2.0: "Kilroy 2.0 is here. Kilroy 2.0 is everywhere."
Into the Darkness, King Swemmel of Unkerlant is inordinately fond of 'efficiency' in all things.
Ciaphas Cain: "If I had known (X) was going to happen, I would have shot (Y) myself."
Lieutenant Villain Dance has a strong tendency to think or say "Never happen!", as in "it will never", when he considers failing in his duty or being shot down.
Pseudonymous Bosch's Secret Series (The Name of This Book is Secret and sequels) has Max-Ernest. How 'bout that?
Rumo, a minor character in The 13 ˝ Lives of Captain Bluebear, at one point tells the eponymous character that he's not good with words when trying (and failing) to explain a situation. When he becomes the main character in the following book, Rumo & His Miraculous Adventures, "I'm not good with words" has become his catchphrase, said whenever he's asked to explain or elaborate on something.
Herman Melville's "Bartleby, the Scrivener" practically never says anything other than "I would prefer not to."
Warrior Cats: "Mouse dung!" as an exclamation of frustration.
Dinotopia: "Breath deep, seek peace" or the Skybax riders' variant. "Breath deep, fly high, seek peace" or simply "Fly high, seek peace".
In the third book of The Hunger Games, Peeta often asks "Real or not real?" thanks to the Mind Rape he suffers at the hands of the Capitol. Haymitch also calls Katniss "sweetheart", mostly to annoy her.
A frequent comment of Mrs. Bird in Michael Bond's Paddington Bear series was "Bears always land on their feet."
In Clint McCullough's Nevada, the main character, Meade Slaughter, when surprised by something, says "I'll be damned" so much that after it's his only response three times in a row, his daughter in law lampshades it: "Meade, if that's your only input, I might as well be talking to the wall."
In The First Law there's "Say one thing for Logen Ninefingers, say he's X" and Glokta asking himself "Why do I do this?"
Song at Dawn: Emerganda is fond of the phrase 'Tort-n’avetz', i.e. "You are wrong." This is acknowledged in-universe.
In The Bible, anytime an angel shows up, it's almost guaranteed that the phrase "Fear not" will appear.