The earliest reference I can find to the saying in its modern form is in the Baptist Magazine, 1815, in an essay simply credited to "T.G." of London.
Ultimately the idea tracks back to Cicero's "Tusculan Disputations", though not in such a terse form (he writes of the ears and nose also being windows to the soul).
TG appears to have been one of many 19th century writers who alluded to the Cicero quote, such as William Hetherington in "Branthwaite Hall and other poems"
Open thine eyes — bright windows to the soul —
But there is no clear-cut famous originator (and certainly not Shakespeare or any of the other usual suspects people pin unknown epigrams to).
Baptist Magazine http://books.google.co.uk/books?id=kEwEAAAAQAAJ&pg=PA99&dq=%22The+eyes+are+windows+to+the+soul%22&lr=&as_drrb_is=b&as_minm_is=0&as_miny_is=1600&as_maxm_is=0&as_maxy_is=1900&as_brr=0&as_pt=ALLTYPES&client=firefox-a
· 1 decade ago