The fruit of the tree of knowledge of good and evil is not an apple. In fact, it's never named in the text. Over the years, it has been identified with many different fruits, including figs, grapes, pomegranates, pears, mushrooms, and wheat.
For more information, check out Google Answers: Forbidden Fruit of Eden, Mythical Plants of the Middle Ages, or Wikipedia. There is also a good summary of this topic in the book In the Devil's Garden: A Sinful History of Forbidden Food by Stewart Lee Allen.