"The Kids Are Alright" is the name of an album, song by and a documentary on The Who.

Dean: Gumby girl... Does that make me Pokey?
Gumby was a stop-motion/claymation kids' show. Being made of plasticine, Gumby was exceedingly flexible. His best friend was a red plasticine horse named "Pokey".

Lisa says that a blood test showed that Dean is not Ben's father. This could have more than one meaning. A DNA test requires genetic material (such as fresh hair) from the possible father. Lisa may not have had access to Dean's genetic material, but if she obtained DNA from another man who was in fact Ben's father, she could eliminate Dean. Alternatively, if Lisa knew Dean's blood type and her own, she could compare them to Ben's blood type to determine if Dean was a candidate to be Ben's father. Though it could not conclusively prove paternity, such a test could eliminate someone with a blood type unrelated to Ben's.

Annette is reading "The Historian" by Elizabeth Kostova, a novel that riffs on the story of Dracula

When Sam is checking into Mary's friends at the end of the episode, he asks about:
-a fire that happened on November 24th 2006 in Lawrence.
-Robert Campbell who died on the 19th of July 2001. July 19th is Jared Padalecki's birthday.
-someone named "Hardecker" (or similar)
-a woman called Wallison
- Ed Campbell

Ruby: Ding Dong, the demon's dead.
This line comes from the musical The Wizard of Oz, where it originally is "Ding Dong, the witch is dead" and referres to the Wicked Witch of the West.

Ruby: "Doesn't change the fact that you're special, in that Anthony Michael Hall ESP vision kind of way."
Anthony Michael Hall plays Johnny Smith in The Dead Zone, a man who could see the future by touching someone. The show is based on a novel by Stephen King.

Lisa Braeden appears again, in an idyllic picnic setting in Dean's subconscious in 3.10 Dream a Little Dream of Me. Dean later goes to say goodbye to her before his plan to say yes to Michael in 5.17 99 Problems. Sam catches up with him while writing a farewell letter in a motel room in Cicero, Indiana in 5.18 Point Of No Return, saying he figured Lisa Braeden would be one of the stops on Dean's farewell tour. Sam makes Dean promise he will go to Lisa after they beat Lucifer and live a normal 'apple pie' life. Dean returns to her at the end of 5.22 Swan Song. In the season 6 premier Dean has been living with Lisa and Ben for a year.

The woman dumping her car in the lake with her daughter locked inside could be a parallel or reference to the Susan Smith case

Ruby: Yeah. Generation of psychic kids, yellow-eyed demon rounds you up, Celebrity Deathmatch ensues. You're the sole survivor.
Celebrity Deathmatch was a comedy show on MTV in which claymation celebrities would fight each other to the death, with often grisly results.