A secret weapon was any person or object which gave one side of a fight or game an advantage over the other.
In 2269, Spock reasoned that if the Slaver weapon was a tool used by spies, the Slavers would have wanted it to remain a secret weapon. (TAS: "The Slaver Weapon")
In 2374, Zek described the persuasive Ishka as his secret weapon in an upcoming meeting with the Ferengi Commerce Authority to discuss the profitability of women and get him re-instated as Grand Nagus. (DS9: "Profit and Lace")
In 2375, Benjamin Sisko described his son Jake "The Slider" Sisko as the Niners' pitcher and secret weapon. (DS9: "Take Me Out to the Holosuite")
Also that year, Tom Paris cautioned Kathryn Janeway that villains such as Doctor Chaotica often had tricks, like trapdoors and secret weapons. (VOY: "Bride of Chaotica!")