What makes this question so difficult is the sense of tradition that some comics have. For instance in Batman or Spiderman it would be tough to permanently kill off a villain that has been around for the history of hero; in some ways the villain has helped define what the hero is all about. To kill the villain is to kill part of the hero and thus part of the book. In a way some villains are part of the fabric of a book.
However in some cases villains in books, usually more independent books, help define the "goodness" of a hero by their ultimate demise. We see this often in the movies, especially Batman movies where the ultimate goal is to overcome a villain. The ultimate goal in comics is to tell a story and sell more comics. There is no sense of permanent closure in comics. I mean Blackest Night as good as it was led to Brightest Day, which will lead to another story and all the while we can pretty much guarantee that Sinestro will probably be around.
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