Wikipedia

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

Alternative forms

cup o' joe cuppa joe

Noun

cup of joe (plural cups of joe)

1. (chiefly US, idiomatic) A cup of coffee.

In volume I, chapter xvi of Dickens' Great Expectations, the following is written: "When, at last, she came round so far as to be helped down stairs, it was still necessary to keep my slate always by her, that she might indicate in writing what she could not indicate in speech. As she was (very bad handwriting apart) a more than indifferent speller, and as Joe was a more than indifferent reader, extraordinary complications arose between them, which I was always called in to solve. The administration of mutton instead of medicine, the substitution of Tea for Joe, and the baker for bacon, were among the mildest of my own mistakes."

Read more: Why do people call a cup of coffee a "cup of joe"? | Answerbag http://www.answerbag.com/q_view/15444#ixzz2EAclIoX0

While it all sounds like fun, the true origin (yes I was there, yes I'm old)was from word games that were very popular in the 30's and 40's "give us some java Joe" because it rolled off the tongue, it became the phrase of choice and the chuckle was that it didn't matter if the servers name wasn't Joe .. and it became cute to shorten it to give us some, Joe ... then just give me a cup of Joe.

Yours trulyKilroy

Post Script:Keep in mind we called Germans, Gerry and the Asians/Chinese, Charlie. Word play continued past WWII ... Joltin Joe DiMaggio and jumping Joe DiMaggio, think it's safe to say it still is an American pastime to play with words.

Read more: Why do people call a cup of coffee a "cup of joe"? | Answerbag http://www.answerbag.com/q_view/15444#ixzz2EAdMrmJR

I don't mind the name Joe, but how about we quit using it out of context all the time. I hate hearing, the average Joe, Joe six pack, Joe blow, a cup of Joe, etc. etc. etc.