Throughout the publication history, two strips have gone unreprinted in part or in whole, and two others were altered.
5/23/87
The unpublished May 23 comic
The strip for May 23, 1987 was reprinted in The Essential Calvin and Hobbes, but missing in Something Under the Bed Is Drooling.
In the strip, Calvin drops a teabag into a glass full of ice cubes, hoping to make iced tea.
11/28/85
The alternate strip (corresponding article details significance in syndication) of November 18, 1985. The original was never reprinted, whether in the first printed collection, the first treasury or even The Complete Calvin and Hobbes; all of these feature the alternate strip instead.
Alternate Format strip
The Alternate format strip was a strip from 1988/08/28. It was orignially printed horizontally in newspapers, but was redrawn vetically for the books. It was not reprinted in the original format until Calvin and Hobbes: Sunday Pages 1985-1995. (link is original format)