Spy Ship

Not James Bond/Sydney Bristow, although that's one for The Ship Yard...

A vehicle, in whatever medium, that looks like a civilian one, but is actually there to gather intelligence.

Film

 * As a Long Runner series of movies about spies, James Bond films of course have several examples:
 * An odd variation in The Man with the Golden Gun. James Bond discovers that the partially sunken RMS Queen Elizabeth in Hong Kong Victoria harbor has been turned into a British listening post for spying on the Chinese.
 * For Your Eyes Only has one accidentally fish up a Sea Mine and sink.
 * This goes back to Dr. No: Quarrel runs a simple fishing boat, but he helps out secret agents all the time.
 * The Final Countdown has the USS Nimitz task force shadowed by a Soviet-flagged "fishing trawler" that isn't doing much fishing.

Literature

 * Polar Star by Martin Cruz Smith. The protagonist discovers that the Soviet factory ship he's working on is broadcasting fake submarine signals meant to be picked up by an American spy vessel—one of the trawlers that provide their fish.
 * Tom Clancy's Without Remorse has Russian "fishing trawlers" following a fleet battlegroup on a highly classified and sensitive mission. Fortunately, they're known to be gathering intel and are easily fooled.

Western Animation

 * The Simpsons featured one with the letters F-B-I painted prominently on the side. (The letters stood for "Flowers By Irene".) Cue the line, "I wonder why that [moving van / florist's van / pizza delivery van / whatever] has been parked there for two weeks," or similar, whereupon the van instantly screeched away and was replaced by another (that was just as suspicious).
 * "Homer the Father", a 2011 episode had a series of these, each of them having the initials of an American government agency but standing for something completely different (CIA = Chinese Intelligence Agency, FBI = French Bureau of Investigation, and ATF = A-Team of Finland).

Real Life

 * Many navies do it:
 * The USSR had at least ten types of these, such as the "Okean" and "Primorye" classes. Much of their commercial fishing fleet was, according to The Other Wiki, also engaged in spying ops on the side.
 * USS Pueblo
 * Before WWII, a small Japanese fishing boat was actually mapping the coast of Southern California and northern Mexico, and listening to radio signals.