According to Cecil Adams in his column, The Straight Dope, (and every other web site I can find agrees with Cecil):

'"Little Goody Two-Shoes" was the heroine of a children's story of the same title, first published in 1765 and often attributed to that favorite of English graduate students everywhere, Oliver Goldsmith. The story, such as it is, concerns a poor waif who has somehow managed to make it through life with only one shoe. Finally rewarded with another, she scampers over hill and dale pointing at her feet and crying "Two shoes! Two shoes!" in so cloying a manner that her name has lived through the ages as a symbol of puerility. "Goody" is a contraction of "Goodwife," a form of address roughly equivalent to our "Mrs.," and now archaic.'

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