When Sam and Dean first encounter Cole's spirit, Sam tries to tell Cole that he is dead, to which Cole replies "Yeah, I know that, Haley Joel." This is a clear reference to The Sixth Sense (1995), which starred Haley Joel Osment as a kid who could communicate with ghosts.
When Sam offers Dean an aspirin for his concussion, Dean says "no thanks, House." This is a reference to the procedural doctor drama 'House, M.D.', which was very popular at the time. It followed the exploits of Dr House, a brilliant but very rude and taciturn doctor who was addicted to Vicodin.
When Sam suggests that they find and speak to the last person to die, Dean says, "Last I checked, Huggy Bear ain't available." He is referring to the confidential informant character on the 1970's TV crime show "Starsky and Hutch."
Just before Alastair performs the ritual to break one of the 66 Seals, he hints at the existence of Death, one of The Four Horsemen of the Apocalypse. He claims an "old friend" loaned him his scythe, and "he doesn't really ride a pale horse, but he does have three amigos." This is also an acknowledgment to the other three horsemen; Pestilence, War and Famine.
Sam tells Dean that he's not just an average joe -- no Joe the Plumber. He is talking about the conservative activist/plumber who engaged Democratic presidential candidate Barack Obama on the topic of small business taxes during a campaign stop in Ohio in 2008.