(from the Coffee and Caffeine FAQ)
Where did the term "cup of joe" come from?
Legend has it that the origin is a follows:
The U.S. Navy used to serve alcoholic beverages on board ships. However, when Admiral Josephus "Joe" Daniels became Chief of Naval Operations, he outlawed alcohol onboard ships, except for very special occasions. Coffee then became the beverage of choice, hence the term "Cup of Joe."