OK. In another post you or your son said that you started the bidding at what the game owed you?. So if that's what it sold for, you haven't lost anything.
I think what John said pretty much sums it up. If it was desirable, you would have had a bunch of people bidding on it.
Sorry to be blunt. But waterworld is a terrible game (yes i've played one) There is no way you'd get 3k for one of those. To be honest, if you started the bidding at 99 cents there would have been a good chance that it finished below what you actually got for it.