The scene with Steve waking up, disoriented, in an ice-filled bathtub, with Roger about to harvest one of his kidneys for profit is a reference to the urban legend where travelers are drugged and one of their kidneys is harvested.
When Steve stands up from the tub, part of his stomach is labeled "sweetbreads," indicating that Roger misunderstood Hannibal Lecter's labeling in Red Dragon.
When Roger explains his theory about Bin Laden to Steve, his room is littered with magazine and newspaper clippings connected by string in a nonsensical fashion. This is a reference to a similar scene involving John Forbes Nash in A Beautiful Mind.
George Bush's choking on a Hot Pocket parodies a real-life incident where he choked on a pretzel. 
When President Bush is discovered drunk he says that his wife would run him over is a reference to an incident where Laura Bush was in a car accident where a friend was killed.
When President Bush is reciting all the alcoholic drinks he made or drank at Hayley's age, it's a reference to the fireworks scene in Joe Dirt.