Referenced in an SUV commercial, which shows four guys excitedly setting up a campsite, until they hear banjo strings... Then it shows them piling back into the car and peeling out.
Dazed and Confused: When O'Bannion is paddling one of the new freshman students, he tells them to "squeal like a pig".
The Descent has a ton of homages to it. There's the premise (a same-gender group - although, this time, all-women) go spelunking in the North American Southern wilderness and find out they got more than they bargained for. More specific examples is Juno's red suit and the white water rafting scene that opens the film.
At the end of The One, a prisoner in the penal dimension the Big Bad was sent to notes "he's got a pretty mouth." However, the Big Bad is a superpowered martial artist who's determined to make everyone in the prison his bitch, not the other way around. And then proceeds to fight everyone as the credits come in.
Zombieland: Tallahassee draws a zombie's attention by playing "Dueling Banjos" on... well, a banjo. He then kills the zombie with the banjo. Plus, he says "You got a purdy mouth," just before he banjos the zombie.
Irish comedy Father Ted homages the banjo duel in a completely random scene — complete with a man dancing along.
In an episode of The Golden Girls, Blanche, who's from the Deep South, misinterprets Rose's statement that she was "rejected by Uncle Sam" (i.e., not allowed to join the military) as though she was actually romantically rejected by her uncle, saying that it just wasn't meant to be, unlike if it was maybe her cousin, wherein the relationship might've gone somewhere. Dorothy promptly asks if any of Blanche's relatives appeared in Deliverance.
Also referenced in Kevin & Kell where a character is arguing that the lack of hunting is not causing inbreeding of prey species... followed by someone identifying the music of the scene as Dueling Banjos.
Codename: Kids Next Door: The tuba battle between Numbuh 1 and Willard in "Operation: O.O.M.P.P.A.H." is one big reference to the banjo duel scene.
The kids' show Cow and Chicken had a scene where Chicken is paddling a canoe down a river, and a creepy hillbilly is laughing and commenting on his "Purty beak", Chicken then starts panicking and rowing away faster.
Hillbilly: You paddle good boy! You better paddle REAL good!
In the Futurama episode "The Deep South", Bender hums a few notes from "Dueling Banjos" when he is first introduced to the lost city of Atlanta (no, not Atlantis, Atlanta).
Harvey Birdman, Attorney at Law turns the dueling banjos into a contest between Mentok and Shado to see who can pull off the best mind tricks.
One episode of Megas XLR has a piece of music called Appalachian Banjo Duel.
In the gym episode of Rocko's Modern Life, Rocko gets on a rowing machine and accidentally sets the difficulty level to "Deliverance". The computer tells him "We gonna make you squeal, piggy!" (Luckily, in this case it involves making a pig laugh by tickling it with a feather, which is terrifying enough for Rocko).
In the Rugrats episode "Family Reunion", a banjo plays in the background as Emmet tells Angelica "Wanna rassle? Bet I can make you squeal like a piggy"
In The Simpsons episode "Boy-Scoutz 'n the Hood", Bart's Junior Campers rafting group (led by Ernest Borgnine) gets lost and winds up drifting through a river in the woods; mountain men are seen in silhouette along the shoreline while the opening strains of "Dueling Banjos" play.
