Ghost Ship makes you place two cards back on deck. With a Wishing Well in your hand, you can draw back the first card and then successfully wish for the second. You’re still hurt by the attack, but it basically leaves you with your original hand minus the Wishing Well—a small price to pay against an otherwise crippling attack.
Scout similarly counters Ghost Ship, because you can place your Victory cards back on your deck and vacuum them back into your hand with the Scout.
In theory, Wishing Well and Scout would also be a counter to multiple Bureaucrats played against you. But in practice, Bureaucrats are usually weak enough that you can just ignore them rather than buying Wishing Well or Scout to counter it.