Actually, they've done a number of clone saga references in the last couple of years. Peter mentions Ben Reilly a number of times in Mark Millar's run (to the point where I thought that, since the story was a take on "Hush", that Ben Reilly was going to be the evil mastermind ala Jason Todd) and during Civil War Peter's public alias as a teacher is "Ben Reilly". The principal compliments Peter by saying "I wish we could clone you" to which Peter responds, "No, you really don't want to do that."