Wordwizard.com has several explanations from different sources for this expression, which is used to describe defeating someone decisively. As William Safire explained in the New York Times, the phrase begins with “clean,” which was applied to the victims of thieves or gamblers who had been drubbed, defeated, and/or wiped out. The “clock” probably comes from the fact a clock has a face, and “clock him one,” refers to hitting him in the head. Brewer’s Dictionary of Modern Phrases & Fable has a similar explanation saying that the expression has a military origin from World War II, and that, “A person’s face is probably their face…” Cassell’s Dictionary of Slang speculates it might be railroad jargon referring to applying the airbrakes and bringing the train to a sudden stop. “The ‘clock” in question is the air gauge, which on halting, immediately registers zero and is thus ‘clean’.”