In the world of comics books, a 'one-shot' is a single standalone comic or graphic novel that isn't part of a regular series. If popular, these may serve as a launch point for a future series. Sometimes they exist as a way to riff on an existing character or concept by presenting them in a new context or way. They may simply be a self-contained story, such as the classic Batman: The Killing Joke graphic novel. Alternate origins are a popular sub-type, such as the Superman-in-the-Soviet-Union story Superman: Red Son (actually a three-issue series, collected in a single graphic novel). Similarly, the well-reviewed Marvel graphic novel Marvels (once again, from a limited series comic) presents things from the perspective of a photojournalist, rather than the usual hero-centered approach.
Crossover between publishing houses are fertile grounds for one-shot team-up books, such as Batman with Captain America or Judge Dredd, or even such outré concepts as Archie Meets the Punisher (yes, really).
By contrast, a "done in one" story is a single issue of an ongoing series that tells a single, standalone tale. This was the norm in the early days of comics before long-running story arcs and complex continuity arose in the 1970s and 1980s. Sometimes the two terms are used interchangeably, most notably in "best one-shot" listings.