If a crime is committed in international waters and the vessel is not registered to any country who punishes the perpetrator?

Generally speaking, it would be the country that the person you - lets say killed, in this instance, which would want justice for what you did - so whenever you made landfall and were discovered to have killed that person, it would probably look something like: Landfall country investigates, they discover the origin of your victim, extradite you to their country to be charged with murder. If it was just you and another person spawning in on a deserted island or boat - no origin or way to prove where either of you are from? Just don't say anything and you'll get away with it - as the last person standing, your morality dictates right and wrong.