cup of joe
There is an attribution to Josephus Daniels (1862-1948) who, as Secretary of the U.S. Navy under President Woodrow Wilson in 1913, was said to have abolished the officers' wine mess. And thus coffee became the strongest drink aboard navy ships known as "a cup of Joe".
This theory does not stand up to scrutiny.
The most likely source is as a shortened form of 'a cup of jamoke' - which was a common reference to coffee, its being a compound of Java and Mocha. There are examples of the jamoke usage throughout popular culture including in the Preston Sturges movie Hail The Conquering Hero (1944).
For more see: http://www.snopes.com/language/eponyms/cupofjoe.asp