Knuckles were joints in between one's finger bones.
In 1944, Carmine threatened to remove Silik's teeth with his knuckles (i.e. punch him in the mouth, thereby knocking out his teeth). (ENT: "Storm Front, Part II")
In 2269, Adam sang, "Gonna crack my knuckles and jump for joy. I got a clean bill of health from Doctor McCoy." (TOS: "The Way to Eden")
In 2369, a newly employed Sarda rebuffed Quark's sexual advances, telling him that although she'd wear her dabo girl costume and entertain his patrons, he could "keep his Ferengi knuckles to himself." She related this conversation to Benjamin Sisko, noting that Quark claimed pleasing him was part of her employment agreement. (DS9: "Captive Pursuit")