score:2
The book Brian Z mentions claims the 17th century:
http://www.nytimes.com/books/97/12/07/reviews/971207.07mckittt.html Grafton traces the history of the modern footnote to rather an unlikely quarter -- from Ranke back to David Hume in the 18th century, then to Pierre Bayle and Jean Le Clerc in the late 17th.