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.
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".
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 not-so-flattering light. The married-with-child Anthony, instead of taking Elizabeth to the police to report her attempted rape, goes on an utterly inappropriate diatribe about how he loves Elizabeth and yet wants her to put her entire life on hold and wait for him. Why? Because Anthony had forced his wife to have a child she did not want and Anthony did not want the scandal that would ensue if he left his wife for Elizabeth, after forcing her to become a mother against her will.