Daniel "Sempere"
The main character has a symbolic name. His last name is derived from the Latin word for "forever" or "eternity." Perhaps this was done on purpose by the author as a sign to the reader that the principles of the story technically apply to any human life, from now until the end of time. Why? Because the nature of life is always both positive and negative, as Daniel learns.
Carax as a symbol for innocence
Daniel is wise, so he doesn't have to suffer a dark fate to learn the worst about life. Because he is an avid reader, and because he is empathetic (he tries to understand what other people are really feeling), he gets to learn from other experiences than his own. That means that Carax's life is also a symbol for Daniel's loss of innocence. As he learns the horrible fate that Carax endures, he understands fate better. Carax is a symbol for lost innocence because the horror of his life turned him into his own worst enemy.
Penelope as the symbol of desire
Suppose Daniel's research into the life of his favorite author was done in an attempt to learn something about life. In that case, Penelope's story teaches Daniel something he might not want to learn. It teaches him that life is not about getting what we want, because if that were the case, perhaps Carax and Penelope could have been born. But at the same time, Daniel sees that he is lucky to exist at all—Penelope would have named her son Daniel, but both she and the child died. Not exactly a picture of "getting what she wanted."
The motif of death and remembrance
The symbols most associated with this motif in the novel are the "Cemetary of Forgotten Books," and the untimely deaths of Penelope and her unborn child. Since cemetaries are for the interment of the dead, and since Daniel "saved" a book from its own death by reading it, by loving it and cherishing the lessons it taught him—perhaps that is the book's way of saying that Daniel rescued the legacy of Carax, and the Daniel that Carax never was able to father. In fact, Daniel names his son Julian—a nod to the same idea.
The symbology of evil
When Penelope cries out for help, her own parents ignore her, which is archetypal because it's so extreme. For her own parents to abandon her is the height of betrayal, since parents have a natural obligation to their children, and they allow her child to die with her, so they are as evil as could be, because they let harm befall a child, their own flesh and blood no less. They represent the forces of infidelity (because the affairs are treacherous), deception (because they won't explain themselves to Penelope), and malice (because they ignore her pleading).
