The title of the episode can be taken two ways: First is the obvious reference to the theme ingredient - dark chocolate. Second, since this was the very last show of the series, it is a way of saying "[Last one out,] turn off the lights."
This is the only episode that doesn't end with "See you next time...on 'Good Eats'." Instead, Alton closes with, "Stay dark, America," snaps his fingers and scene fades to black.