A cookie jar was a container for storing cookies.
In 2151, Trip Tucker used the metaphor of being "caught with one's hand in the cookie jar", telling T'Pol he felt like he was had been thus caught, after he confessed to looking at her private letters. (ENT: "Breaking the Ice")
In the script for "Family", Marie Picard walked in on Jean-Luc and Robert Picard, both drenched in mud after a fight, at the dinner table eating cheese and fruit, and "they look up like children caught with their hands in the cookie jar". [1]