There is a missing strip of Calvin and Hobbes that was printed only in half of the papers running the strip, while the other half had another unique strip, which was never reprinted in the book collections. Here they are.◊ (It's likely this was done so as not to encourage child readers to actually try to bathe in the washing machine.)
At one point in Floyd Gottfredson's Mickey Mouse newspaper strip, Mickey, believing that Minnie is leaving him for another man, sinks into a depression so deep he spends a week attempting to commit suicide. After a week of failure, he decides he might be overreacting a little. You can imagine that this sequence is left out in the reprint of the story arc, and it is completely absent from D23's newspaper strip archive.
It was left out in a 1998 comic book reprint and on the D23 website, but the relatively recent Floyd Gottfredson Library reprint (2011) left the sequence intact.
Traditionally, most newspaper comics were not re-published in complete form when packaged as books, leading to many strips that were published once in papers and never seen again. (Among other reasons, it allowed editors to cull out weaker or more controversial strips.) Peanuts is a good example — a large percentage of strips were never republished in book form until the release of the "premium" complete collections.
Pearls Before Swine may very well be the only work of fiction to have a Lampshade Hanging about a Missing Episode. Pig once tried digging to the other side of the Earth to a fictional country and he says that the original comic strips where he named a country "China" were removed. They were shown in one of the Pearls books. In fact, many Pearls books contain comic strips that were not printed because they were deemed too offensive or simply not funny by the creator himself. These include one where Pig talks about "ho's" (referring to Ho Chi Minh) or other edited versions where the character Cathy is beheaded.
On April Fools' Day 1997, almost every syndicated cartoonist traded places with another. Bill Amend (FoxTrot) drew that day's Zippy the Pinhead while the Nancy team took that day's FoxTrot. The strip that they drew does not appear in the compilation Welcome to Jasorassic Park, though; in its place are the chewed-up corners of the strip and a flock of "Quincyraptors" (a reference to a Jurassic Park pastiche in that same compilation, wherein each dinosaur resembles Quincy).
For some reason, the Garfield trade books never covered May 2–5, 1990 — Garfield Takes Up Space stops on May 1, and Garfield Says a Mouthful starts on May 6. This is also true of the several reprints of both books, although those four strips are available on garfield.com.
In terms of other works by Jim Davis, the last 50 strips of U.S. Acres were never published in book form in the USA. The last strips (except for a Sunday strip where Wade crushes Booker's playset of a barn) were published in the United Kingdom in the book "Orson's Farm Cuts the Corn".
Davis' pre-Garfield strip Gnorm Gnat is believed to be almost completely gone from existence. At last report, Davis himself doesn't mind one bit.
When Lynn Johnston compiled a variety of strips together by story arcs on the "For Better or for Worse" Web site, the section featuring Anthony saving Elizabeth from being attacked by a would-be rapist omits a series of strips that paint Anthony in a very unflattering light. Instead of then taking Elizabeth to the police to report her attempted rape, he first announces that "he's never had anything to fight for until now" (this, from a man with a wife and brand-new daughter), then takes her to a park and proceeds to go on a whiny diatribe about how horrible his married life has become ("I have no home!"). From the context, this is mostly because his wife refuses to be a stereotypical stay-at-home mom. And all of it is explicitly an effort to guilt-trip Elizabeth—remember her, the young woman who's just been violently assaulted by her stalker?—into waiting for him. Apparently Johnston designed the entire assault plotline simply as a means to give Anthony an old-fashioned Big Damn Heroes moment, complete with Standard Hero Reward, and until the inevitable backlash erupted was completely oblivious to the fact that she was instead turning him into a Jerkass of the highest order.
Angus Og: Sadly many strips from this title are missing entirely, with not even the author, Ewen Bain's, estate having copies of them; mainly the gag-a-day strips, the longer arcs are a little more complete. Newspaper comics were seen at that time as a disposable medium. A few compilation books do exist though, with the surviving storylines.
Mexican comic strip El Cerdotado: Strips 80 to 83, originally published in "El Diario de Monterrey" newspapper, has been left outside from the compilation as the autor think they was "very lame" (Pasarse de chafas), and are currently unavailable.