A transponder was a type of tracking device on board a starship, starbase, or other spacecraft, which broadcast a signal identifying that craft by name, design, and allegiance. This allowed for easy recognition of craft, especially at distances where visual inspection or accurate sensor readings were not possible.
Transponders could be deactivated or have their details forged, however, so the existence or absence of a transponder signal was not proof-positive of a craft's identity or existence. For this reason, transponder signals could include some kind of code proving to those "in-the-know" that the signal was genuine.
In August of 2151, Transponder 4 of Echo 1 was used as relay for a communication between Admiral Maxwell Forrest at Starfleet Command on Earth and Captain Jonathan Archer aboard Enterprise. (ENT: "Fortunate Son")
In 2153, Osaarian pirates were equipped with small transponders. Usually, on raiding missions, each Osaarian had one of the devices attached to the right shoulder of his own uniform. However, the transponders could be quickly detached and applied to other items, such as cargo selected for transport. (ENT: "Anomaly")
In 2369, Chief Miles O'Brien and Lieutenant Jadzia Dax searched for the crash landed runabout USS Yangtzee Kiang and were even unable to find the transponder signal of the runabout. (DS9: "Battle Lines")
Later in 2371, O'Brien planted a transponder on a Flaxian ship that visited Deep Space 9 that year. It was detectable within a range of a half-light year, however, the ship was destroyed before it could be put to use. Following the destruction of the ship, O'Brien was nevertheless able to analyze the telemetry from the transponder and discovered an interference pattern in the transponder's signal, indicating the ship was destroyed by a forced neutrino inverter. (DS9: "Improbable Cause")