from Brewer's Dictionary of Phrase and Fable

Yankee Doodle is Nankee Doodle (Oliver Cromwell), who went to Oxford “with a single feather fastened in a macaroni knot,” whence the rhyme-

The brigade under Lord Percy marched out of Boston playing this air “by way of contempt,” but were told they should dance to it soon in another spirit.

There was no one person to whom this term was given. It was certainly a song popular in the United States of America before the War of Independence. It is now regarded as one of America's national tunes.

How the name Yankee Doodle came about is not clear. It is, however, generally believed to have been due to the English surgeon named Richard Shuckburgh. He seems to have introduced the term in 1775 in some verse he wrote that ridiculed soldiers in gaudy uniforms.
The origin of this song isn't certain. I've heard the French and Indian War, a Spanish sword dance, Dutch peasant song, a work song from French vineyards, from the Basques, the Hungarians, the Irish, or from the English nursery rhyme, "Lucy Locket".

The song was, of course, very popular during the U.S. Revolutionary War, used by the British to make fun of the Rebel Scum and then by the Rebel Scum. Now a patriotic All-American tune. It's actually a good song.

There are many versions of the and hundreds of verses total, but here's the most common version:

Father and I went down to camp
Along with Captain Gooding
And there we saw the men and boys
As thick as hasty pudding.

Chorus
Yankee doodle, keep it up
Yankee doodle dandy
Mind the music and the step
And with the girls be handy.

There was Captain Washington
Upon a slapping stallion
A-giving orders to his men
I guess there was a million.

Chorus

And then the feathers on his hat
They looked so' tarnal fin-a
I wanted pockily to get
To give to my Jemima.

Chorus

And then we saw a swamping gun
Large as a log of maple
Upon a deuced little cart
A load for father's cattle.

Chorus

And every time they shoot it off
It takes a horn of powder
It makes a noise like father's gun
Only a nation louder.

Chorus

I went as nigh to one myself
As' Siah's underpinning
And father went as nigh agin
I thought the deuce was in him.
We saw a little barrel, too
The heads were made of leather
They knocked upon it with little clubs
And called the folks together.

Chorus

And there they'd fife away like fun
And play on cornstalk fiddles
And some had ribbons red as blood
All bound around their middles.
The troopers, too, would gallop up
And fire right in our faces
It scared me almost to death
To see them run such races.

Chorus

Uncle Sam came there to change
Some pancakes and some onions
For' lasses cake to carry home
To give his wife and young ones.

Chorus

But I can't tell half I see
They kept up such a smother
So I took my hat off, made a bow
And scampered home to mother.

Chorus

Cousin Simon grew so bold
I thought he would have cocked it
It scared me so I streaked it off
And hung by father's pocket.

Chorus

And there I saw a pumpkin shell
As big as mother's basin
And every time they touched it off
They scampered like the nation.

Sources:
http://www.straightdope.com/mailbag/myankeedoodle.html
http://www.contemplator.com/america/ydoodle.html
http://www.contemplator.com/america/ydoodle.html

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