An output shaft is the part coming out of an engine that operates the accessories or transmits the engine's power. This can drive the transmission or the alternator. Typically, an output shaft is terminology used in small engines or farm machinery.
On a typical gasoline-powered, front-wheel drive automobile, the output shaft will be at the bottom of the engine and in the front. This shaft will have a pulley attached to the crank shaft hub that will drive all of the engine accessories. The accessories will be driven via a rubber belt which will be threaded around all of the engine's pulleys.
On rear-wheel drive applications, the engine will actually have two output shafts. One on the front of the engine, which will drive the engine accessories, such as power steering and the charging system. The second will be protruding from the rear of the transmission. This will be the location where the drive shaft attaches and transfers power to the rear end.
Four-wheel drive vehicles will actually have three output shaft locations. One will be at the front of the engine, another will come out of the rear of the transfer case to drive the rear wheels much like in the rear-wheel drive application. The third output shaft will come out of the front of the transfer case and will drive the front tires. These shafts provide the engine's power to three different locations on the vehicle.
In the case of a propeller-driven aircraft, the shaft coming out of the nose cowling provides power to the propeller. On a ship the propellers are driven by a shaft. On farm machinery, the case is not so clear. On farm machinery the implements are driven by the power take off or PTO. The PTO shaft protrudes out of the tractors chassis and the implement's drive shaft is coupled to this shaft.
Motorcycles are unique in that the crank shaft does not power any component outside of the engine. Harley Davidson and Indian motorcycles are contrary to this rule. On these two brands, the engine output shaft powers the transmission via a chain or belt. On all other brands, the transmission shaft powers the rear tire by chain and sprocket or by drive shaft. The transmission receives its power through a gear box running off of the crank shaft.