Chris sez, "The Wisconsin Historical Society has a smallish but excellent gallery of about forty covers from late-sixties underground newspapers. I'm a sucker for Robert Crumb, so Gothic Blimp Works #3 was my immediate favorite, whereas I think Space City's 'psychosurgery' cover will probably haunt my dreams."
(Thanks, Chris!)
See also: Free Press: reproductions of underground papers, 1965-75
Update: Paul sez, "there's a more comprehensive web exhibit (without the same attempt to copyright the images as Wisconsin) at this UConn site."