From a site called answerbag. I really like the comments:
Josephus Daniels (1862-1948) was appointed Secretary of the U.S. Navy by President Woodrow Wilson in 1913. Among his numerous reforms of the Navy was the abolition of the officers' wine mess. From that time on, the strongest drink aboard navy ships was coffee and over the years, a cup of coffee became known as "a cup of Joe".
* jana2005: it is unuseful
* Bibliophile_kg: this is a common story about "cup of Joe", however 2 etymologists on the web disagree. see my entry.
* IAmDeath: Cool!