Here's a very good article, surprisingly from the Daily Mail of all papers, that gives a very clear account of all the troubling details that cast a heavy doubt that either Amanda or Raffaele were involved in the murder. Very interesting read:
Amanda Knox: The troubling doubts over Foxy Knoxy's role in Meredith Kercher's murder | Mail Online
Whatever happened in that house that night did not happen the way the prosecution insisted it did. The only thing that is clearly irrefutable so far is that Rudy Guede was there and that he had sex with Meredith. Everything else, including the accusation that he killed her, is open for debate and speculation. Too many things just don't add up and don't make any sense.