It is thought the nickname "Joe" for a cup of coffee began as a disparaging term referencing Josephus Daniels, the secretary of the Navy during World War I. Interested in imposing a greater level of morality among troops, Daniels banned the consumption of alcohol among other things.
At this time, soldiers began buying more coffee and Daniels' name became linked to the drink. Originally called a "cup of Joe Daniels," the term was subsequently shortened to just a "cup of Joe" and has been in wide use since. Other theories point to the connection of java and jamoke as two of the best coffees around and that the word "Joe" is derived from the joining of the two words.