From Bravo Fleet Infobase
Auxiliary craft are vehicles embarked aboard starships, starbases, and other vessels and facilities which are used for any number of duties, ranging from short-range personnel and cargo transportation, to maintenance, to scouting and scientific missions, and to certain limited tactical applications. These craft are too small for sustained independent operations, but still form a vital part of Starfleet and are ubiquitous throughout the Federation.
Main Article: Personnel Shuttles
Personnel shuttles are the most common form of auxiliary craft used by Starfleet. Made for short-duration missions, these craft generally have warp capability that limits them to an effective range of only a few light-years from their mothership or base, and they typically can accomodate between four and eight people, including their crew. They are most effective at travel within the same star system.
Main Article: Cargo Shuttles
Cargo shuttles are larger than personnel shuttles and are used to move larger quantities of cargo across larger distances than is practical with a cargo train being pulled by a CMU. They are also useful for moving cargo between a ship and a planet when conditions do not allow for the use of the transporter. Their warp engines are generally as limited as personnel shuttles, and so they are most effective at travel within the same star system and most often have a crew of two.
Main Article: Shuttlepods
Shuttlepods are small vehicles that are used for very short range missions, generally for ship-to-surface, ship-to-ship, or station-to-ship transportation of personnel or very small quantities of cargo. They are generally limited to sublight flight and are not suited for missions of more than a day, though they rarely approach even this limit.
Main Article: Runabouts
Runabouts occupy a range of usefulness between a shuttle and a small starship. Generally modular in nature, they are built with the "go anything, do anything" school of thought, which makes them useful for low-intensity missions independent of their base or mothership. With greater defenses, range, and accommodations, these craft are suited for missions of over a week and can be outfitted for even longer missions when necessary. They are more commonly found aboard starbases, though most starships can handle at least one in their hangers.
Main Article: Starfighters
Starfighters are relatively rare within the Federation during peacetime, largely held in storage at starbases and other similar facilities, but they are essentially shuttles with heavier armament, used to defend larger vessels and perform other tactical tasks. While some models have warp drive, they are generally only suited for use in the immediate range of their base or mothership.
Main Article: Maintenance Craft
Maintenance craft are used within shipyards and for EVA purposes on starships to perform maintenance tasks that cannot be accomplished by personnel in environmental suits. These craft are also used to manipulate and stow cargo within starbases and starships.
Starship-Integrated Auxiliary Craft
Main Article: Starship-Integrated Auxiliary Craft
Some starships have specialized docking cradles for hull-integrated auxiliary craft. An example of this would be the large shuttlecraft docked to Galaxy and Sovereign-class starships known as the captain's yacht, or the enhanced runabout docked to Intrepid-class ships known as the aeroshuttle. These craft typically vary widely in terms of their abilities and their functions based on the vessel that they are attached to, but they are rarely found in other contexts.