The Malfoys have an Eagle Owl, and one is used to communicate between Voldemort and Crouch Jr. I really don't think it's the same owl, as the Malfoys were unlikely to be in contact with Voldemort at that point (although I'm sure Lucius knew something was up). Did Crouch Jr. own the owl and keep it at Hogwarts or was it Voldemort's? Or is there a chance it was indeed the Malfoys' owl?
Is there anything significant about it being an Eagle Owls? Have they, in our history, been associated with evil?