Well that does depend on the ship or station in question. Primarily they were used for the impulse engines which were essentially a bunch of fusion reactors strapped together and a nozzle to direct thrust. The power could be fed throughout the ship by directing it through EPS conduits. DS9 had fusion reactors left over from the Cardassians, if I remember correctly, that were used to power the overall station. If my memory is correct then those same fusion reactors could also be used in a self-destruct sequence on board DS9.