"...Was Ben's Father" is a running gag that originated during a playthrough of The Binding of Issac on Video Games Awesome. At one point during the episode, Ben mentions that his mother's doctor had advised her to have an abortion while she was pregnant with him while the gang is discussing horrific childhood memories. Some time later, Fraser mentions that it would be pretty funny/messedup if the doctor who had advised it was actually Ben's father, and because Ben's mother ignored him and gave birth anyway, he gave up his doctorate to become a lab technician. Despite the audacity of the joke, Ben took it in stride and even remarked that the idea would make an interesting miniseries.
Since then, Fraser and co. will take a random person/creature/thing from whatever game they are playing and say "And that *insert person/creature/thing here*...was Ben's father".