Great question.
lemon "worthless thing," 1909, Amer.Eng. slang; from lemon (1), perhaps via criminal slang sense of "a person who is a loser, a simpleton," which is perhaps from the notion of someone a sharper can "suck the juice out of." A pool hall hustle was called a lemon game (1908); while to hand someone a lemon was British slang (1906) for "to pass off a sub-standard article as a good one." Or it simply may be a metaphor for something which "leaves a bad taste in one's mouth."
http://www.etymonline.com/index.php
