Virtually all the ride names, such as "Captain Dinosaur's Pirate Rip-Off" and "Haunted Condos" (which is mentioned as being closed for "annual ghostbusting")
The billboard that says "Send Money to Universal Studios", a particularly hilarious case of a company making fun of itself.
When the Simpsons are being dropped from the "Death Drop" ride, Homer exclaims, "My bosoms are slapping my face!"
During the part when Sideshow Bob is trying to kill the Simpsons with a wrecking ball, Homer stands up out of the vehicle, proclaiming that the rule of sitting down on the ride is "a load of corporate crap!", only for him to get knocked out of the vehicle by said wrecking ball.
Homer (when running away from the now-rolling wrecking ball): Come on ball, you don't want to hurt me, we're both big and round and never finished high school!
When Homer and Marge land on the pirate ride:
Homer: Alone at last!
Marge: Bob's trying to kill the kids!
Homer: It just gets better and better...
Two of the exchanges in the ride's opening scene:
Lisa: I'm scared, dad!
Homer: Sweetie, they won't kill you in an amusement park as long as you have a dime left in your pocket.
Sideshow Bob: There's nothing you can do! You're about to die!
Homer: You sound like my doctor!
When the Simpsons go back into their home, only for it to be revealed that their still on a ride, Kang and Kodos come out, with Kodos saying, "Foolish earthlings! Don't you know all rides must exit near the gift shop?"
During the whale scene:
Sideshow Bob: You've foiled my plans for the last time!
Bart: ...you've soiled your pants for the last time? Haha!
In the queue line, there is a newspaper (titled "The Medieval Times") whose headline reads Lord Farquaad returns from the grave! Still very, very short.
There are several posters throughout the queue line that parody both movies and Disney attractions, ex: The Enchanted Tick Room, Claws (showing Farquaad swimming in the clouds with Dragon about to strike from below), Liar Liar (with Pinocchio in the main role instead of Jim Carrey).
In the pre-show room, there is a large sign parodying the Universal Express Plus system, advertising being tortured as a theme park attraction in of itself.
The imprisoned Three Little Pigs and Pinocchio being baffled that the audience "didn't see the movie", with the latter saying, "It's what happened after the end credits that got us all into this pickle!"
The Pinocchio asks the Magic Mirror to tell the audience "the story". The mirror responds:
Magic Mirror: Sure! *prepares* A long time ago, in a galaxy far, far away... *Star Wars music plays and he rises upwards in a way similar to the opening titles of Star Wars*
Pig One: Oh, I love that story!
Pig Two: Me too!
Pig Three: It's a little bit too episodic for my tastes...
Pinocchio: NO! Our story!
Magic Mirror: Oh, so sorry, I've been feeling really spaced out lately...
During Farquaad's first appearance:
Magic Mirror: Lord Farquaad! My, you're looking rather...pale...
Farquaad: Of course I am, I'm a ghost, you fool!
When Donkey asks (and later attempts to guess) why Fiona is crying:
Donkey: Awww, what's wrong, Princess? You shouldn't be this unhappy until YEARS into your marriage!
Fiona: It's the happiest time in my life...it's just...
Donkey: Oh, wait let me guess, you're overwhelmed by love!
Fiona: No!...I mean, yes...but that's not why I'm...
Donkey: A shrimp platter was bad?
Fiona: No, Donkey! I just...
Donkey: Wait, wait, I got it! You've always wanted a puppy, but all you got was toasters!
Fiona: NO! I'm sitting in an onion! This carriage is one big onion...
Donkey: Oh. Why didn't you say so?
After Donkey's tail is briefly grabbed by a ghost hand:
The exchange when Ooblar is attempting to steal Jimmy's Mark IV and the remote that controls it.
Jimmy: Carl! The remote!
Ooblar: Give me that! Or I'll hurt you...
Carl: Okay. *casually hands it to him*
Jimmy (annoyed): Carl!
Carl: I couldn't help it, Jim. He used some kind of space alien mind-meld on me!
When Jimmy and Carl end up in Fairy World, Cosmo, mishearing what the two are saying, briefly turns Ooblar into a Yolkian Elvis and Carl's hair into bacon (which Elvis Ooblar attempts to eat.)
During the confrontation on the Yolkian Planet, King Goobot brings out Poultra (whom now appears to have a corrosive breath ability) to finish off Jimmy and Carl, resulting in this:
Ooblar: Yes, Poultra will teach you the meaning of- *gets breathed on by Poultra* ...ow.
Shortly after, Poultra accidentally destroys both the Mark IV and Ooblar's egg shell, the latter commenting, "I was hoping he'd go easy!"
When Jimmy and Carl crash-land into Bikini Bottom and encounter SpongeBob and Patrick:
Patrick (gesturing at Jimmy's rocket): SpongeBob, look!
SpongeBob: Wow! A rocket-powered jellyfish!
SpongeBob causes Jimmy to lose control of the rocket when he puts his net around Jimmy's head, and during the ensuing struggle, the wings of the rocket cut SpongeBob's pineapple into several slices, which land in a huge and conveniently-placed can of sliced pineapple. Then there's also this bit of dialogue from SpongeBob:
SpongeBob (while being flung through Bikini Bottom by Jimmy's rocket): Hello, Gary! Hello Larry! Hello Sandy! *crashes through the Bikini Bottom sign* Hello Mrs. Puff! Hello secondary characters!...
King Goobot making the ride vehicles do the chicken dance, which he calls "a fate beyond your worst nightmare!"
Carl using Cosmo's wand to poof up a bunch of llamas, which also results in a blink-and-you'll-miss-it cameo by Dalai Llama.