This article is from the Coffee and Caffeine FAQ, by Alex Lopez-Ortiz with numerous contributions by others.
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."
 
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