The USS Enterprise-E, which was a Sovereign class, had a Captain's Yacht. Even Galaxy and Intrepid class vessels are supposed to have these, but they are never seen or heard about on screen.
What is the purpose of this type of vessel (and of course, why aren't they used more often)? Tactical, cargo, passenger, multi-purpose or captain's personal use? Wouldn't it have been better to simply add a Runabout to the ship's complement of shuttles instead?