The title A Tale of Two Cities is taken from a well-known Charles Dickens novel with the same title. In the novel, a man, learning he is to become the next Marquis St. Everemonde, is desperate to hide this information from his new father-in-law, a Briton who had been imprisoned by the man's uncle years before. Meanwhile, when he must return to Paris on matters of business, he is captured by the members of the French Revolution and sent to the guillotine. The man's life is spared by an acquaintance who takes his place at the guillotine, a British lawyer who bears an uncanny resemblance to the man.
Also, in the official podcast, Damon Lindelof explained that the "two cities" refer to the two "societies" of the Others and the survivors.