Amen was a term which was adapted from the Hebrew language, literally meaning "truly" or "so be it". It was often used to signal agreement with a prayer or a statement.
In dazzled response to Mudd's women arriving on the USS Enterprise in 2266, Doctor Leonard McCoy absentmindedly commented to Montgomery Scott, "Amen to that, Scotty," even though Scott hadn't said anything immediately beforehand. (TOS: "Mudd's Women")
During the Neutral Zone Incursion later that year, Dr. McCoy again stated, "Amen to that." His use of the term was in reply to his commanding officer, Captain James T. Kirk, remarking – while the Enterprise prepared to engage a Romulan Bird-of-Prey in battle – that McCoy's services as a doctor hopefully wouldn't be required aboard the Enterprise. (TOS: "Balance of Terror")
At the funeral of Felisa Howard in 2370, Maturin spoke the final words, to which the assembled funeral party replied with "Amen." (TNG: "Sub Rosa")
In 2372, before a joint Starfleet-Jem'Hadar mission to destroy an Iconian gateway on Vandros IV, Miles O'Brien told the assembled Starfleet personnel that he wanted to survive the mission, contrasting with the disregard for death by the Jem'Hadar. Benjamin Sisko agreed with O'Brien, stating, "Amen. Let's get it done." (DS9: "To the Death")
In 2376, in the Fair Haven holoprogram, the inhabitants of Fair Haven attended mass in a church and ended a prayer with "Amen," before Father Mulligan began his sermon. (VOY: "Spirit Folk")