The DVD version of this episode has an unaired scene that contains a hymn sung by the church's congregation.

{All singing} “God you are so cool. Although, sometimes it's, like, what's the deal? You never answer your cell phone and your messages are often ambiguous. Amen”

Cartoon Network's [adult swim] version aired a scene not shown on the FOX broadcast where in a parody of National Lampoon's Vacation, Christie Brinkley's character drives along side Peter but instead of flirting with Peter gets hit by a semi truck.

Lois: It is so good to be home. You know I wanted us to live in a place with real family values, but values don't come from where you live or who your friends are. They come from inside, from your own beliefs
Peter: I agree Lois. Like for instance if you're watching a TV show and you decide to take your values from that... you're an idiot.
Maybe you should take responsibility for what values your kids are getting.
Maybe you shouldn't be letting your kids watch certain shows in the first place if you have such a big problem with them, instead of blaming the shows themselves.
(looks into camera) Yeah.

There's no mark on the cow after Peter holds the branding iron to him for several seconds

The episode title “Boys Do Cry” is a take off of the 1999 Hilary Swank movie titled “Boys Don't Cry”

Seamus: “Here be a jaunty sea shanty from me boyhood”

Seamus actually plays “Great Balls of Fire” by Jerry Lee Lewis

Herbert auditions with the song “I Know What Boys Like” by The Waitresses

When Stewie is imagining what it would be like to meet Jesus and he allows Stewie to watch him bathe, the commentary for this episode states it may be an allusion to the 1985 movie “Witness” starring Harrison Ford & Kelly McGillis

Jake Tucker auditions with the “William Tell Overture” by Gioachino Rossini.
It is probably most well known as The Lone Ranger Theme

Lois: “And lately this family has been lacking moral fiber, especially you Meg.”
{Cut Away Scene w/ Meg deflated on the couch}
Lois: “Meg! What's happened to you?”
Stewie: “She can't answer you. She can't even talk.”

Reference to a real anti pot commercial from abovetheinfluence.com

Lois: “You marry Billy Joel, it's gonna happen one way or another”

Lois is referring to the fact that Christie Brinkley (the woman in the exploding car) was married to singer Billy Joel from 1985–1994.

Kevin Bacon in 1984's “Footloose”

Peter: “You know they say Chuck Norris is so tough, there's no chin under his beard. There is only another fist.”

Reference to the late 2005 Internet phenomenon of “Chuck Norris” facts

Stewie: “Oh, lovely. A first class ticket to a semen-covered death in the basement”

Reference to the (albeit simplified) circumstances surround the 1996 death of JonBenét Ramsey in Boulder, CO

Dick Cheney: “I'd like you to meet my daughter's husband, Michael”

The joke being, Dick Cheney's daughter, Mary Claire Cheney, is actually a lesbian.

George Bush: “I restored it myself last summer. I was here for 12 weeks. I had to do something”

(Possible) Reference to the fact Bush is the 2nd most vacationed president in history at 418 days as of August 2007. 2nd only to Ronald Reagan.

Sixteen Candles

Chris' line of “Can I borrow your underpants for 10 minutes” & holding them for the group of boys in the restroom is a direct scene from the 1984 movie “Sixteen Candles” starring Anthony Michael Hall & Molly Ringwald where The Geek (Hall) holds up Samantha Baker's (Ringwald) underpants for a group of onlookers

Cowboy: “In Texas, we execute the retarded”

Reference to the fact that in 2000, Oliver David Cruz a man sentenced to death for the 1988 abduction, rape and fatal stabbing of 24-year-old Kelly Elizabeth Donovan, was allegedly mentally retarded.

Cowboy: “Hey! It's Enrico Palazzo”

This line is from 1988's The Naked Gun. It is spoken when Frank Drebin (Leslie Nielsen) impersonates famed opera singer Mr. Palazzo in order to infiltrate the stadium

The family runs to Texas to stay at Carol's house, Lois' sister.
This is the second time Carol is mentioned (although she is not seen) since her first appearance in “Emission Impossible”. It is also mentioned she has remarried after her husband Ted left her in the same episode.

She is not seen again until the Season 9 episode, “Brothers & Sisters”.

This episode is the first time Peter mentions the fact he is retarded since the diagnosis in “Petarded”.