When Lois tells Peter that Brian tried to have sex with her, Peter asks, "Was he bigger 'n me?" This is a quote from the film Animal House.
Stewie says he carved "Brooks was here" in Lois's birth canal on the way out, which is a reference to The Shawshank Redemption.
"Spirit of Massachusetts" originates from a television commercial campaign of the same name from the 80's which promoted tourism in Massachusetts.
During this fight between Peter and Brian, Peter holds a keg above his head with the intent to hit Brian with it, and is kicked in the genitals, at which time the keg falls on his head. This is a reference to Indiana Jones and the Temple of Doom in which the same thing happens to an Indian cult member during a fight with Indiana Jones.
When Herbert gets a bath from Meg instead of Chris, he exclaims "Rats!" in the same manner as Charlie Brown.