My family is planning a trip to visit friends in Ghent in June. We're already planning a day trip to Brugge, but I'm looking for recommendations for an overnight trip or two. My son will be 4.
How about MiniEurope, close to the Atomium in Brussels?
These amusement parks are very kid-friendly, based on a popular Belgian TV show for children... although it may not mean much to your son if he is not familiar with the show. And the websites are only in Dutch and French:
I think Brussels would be good trip as well. Your son will probably get a kick out out of the Mennekan Pis and you can go see his costumes in the city museum. Also, he might enjoy some of the comic murals painted on the city buildings and sculptures located in squares around the city. I would take him to the lobby (but not into) of the Comic book museum - there he can see a few life size statues of characters (including the smurfs).
There is also a wonderful zoo in Antwerp.