Flagship
A flagship is a particular ship in a fleet or task force that carries the "flag officer", the officer who has command of the entire fleet.
Flagships in Star Trek
In TNG, the USS Enterprise is repeatedly described as the "Federation flagship", even when it is not operating as part of a fleet. This indicates that Starfleet uses the term to mean "the best ship in our entire fleet" rather than the command ship of a specific fleet or task force.