There's a few references to Lisa's Subsitute:
-Marge gives Lisa the paper quoting "You are Lisa Simpson". Mr. Bergstrom gave her a similar paper.
-The poster looking for Lisa that says "Free Beer: Now that I got your attention....", which is like the one where Bart's campaign poster says "Sex: Now that I got your attention...".
Lisa said her I.Q. is 159. In "Homer's Enemy", Homer states Lisa's I.Q. is 156.
Lisa: I'm tired. I'm hungry. Red plastic sandals are not good running-away footwear.
Chief Wiggum: Somewhat satisfied? Well, maybe I'll just somewhat find your daughter.
Lisa: Stuffed cabbage? Can you beleive they found a way to make cabbage worse?
Phonics Frog: I agree with your mother. You are a disappointment to Huh-Oh-Muh-Eh-Ur.
Henry: Meet Maggie Simpson, IQ 167.
(Lisa holds up a card that reads "octogenarian". Maggie points at Grampa.)
Lisa: No, that's wrong.
(Maggie points at the dog.)
Lisa: That's right, this says 'dog'.
Homer: We've all learned something today. Never be something you're not, namely food.
(Lisa is dressed as a goth.)
Milhouse: What are you now Lisa? An Oakland Raiders fan?
Lisa: Just because Maggie can't talk doesn't mean she's dumb. Einstein didn't speak until he was three.
Marge: And even then he could only speak German.
Phonics Frog: How-dayr-yew-lee-sa-yew-arh-ah-dis-grayss-tuu-huh-ohh-mm-ehh-ur. (How dare you Lisa! You are a disgrace to Huh-Ohh-Mm-Ehh-Ur.)
Lisa: So… Maggie's NOT a genius?
Henry: Oh she could be… at sweeping up hair!
Homer: That's my baby, JERK!
(Punches Henry leaving him with a bruise on his nose)
Henry: You call that a punch? I felt it, but it was like "so what"?
(Homer punches Henry again leaving a nosebleed)
Henry: Oh, again with the nose. I have a chin too you know!
(Homer punches Henry making him unconscious.)
Moe: (as the butler) Don't worry sir, the maid and I will take him out to the curb. Come on!
Barney: (as the maid) You promised me no one would get hurt!
(Lisa as a stand-up comedian)
Lisa: So... why do they call them field trips? We never go to a field!
Skinner: Not true! Last week we went to a battlefield.
Ralph: I'm bembarrassed for you!
Nelson: The following "Ha Ha" is not from amusement, but a sign of contempt. HA HA!
Henry: You are now qualified to teach at Florida State.
Simon: You call that a punch? I felt it, but it was like "so what?"
Boy: The pig says Oink! The chicken says..
Henry: Stop! I could go to any Chuck E' Cheese in America if I want to hear what animals say. You know what I say? I say next!
(Mother picks up boy and walks away)
Boy: You're a poopie!
Henry: Do you nurse with that mouth?
Lisa: I can't believe I'm jealous of a baby!
Bart: Hey, so am I! When you're a baby, you can just spend all day rolling around on the floor.(sighs)I miss those days.
Nelson: Then roll, baby!
(Bart rolls on the bus floor)
Nelson: Ha Ha! Floor Baby!
Lisa: You're laughing at him for something you made him do.
Nelson: Well… you're gay!
Lisa: People who call other people gay are often covering up their own latent homosexuality.
(Nelson panics and jumps out the emergency exit. He rolls and then gets back up)
Nelson: BULLIES RULE!
Homer: Marge, I always loved you. Bart, you were a worthy foe.
Pimply Teen: Sir, you can't take food into the theater.
Comic Book Guy: Search all you want. You'll never find it all. I'm baking muffins as we speak.
Homer: (snores then presses Phonics Frog button)
Phonics Frog: ZZZZZZZZZZZZZ.
(After getting digested)
Homer: Now Marge, you can't say I never take you anywhere.
Homer: Look what they sent over. A talking dealy. His name is Phonics Frog.
(Homer presses A, B, and C)
Phonics Frog: Ah-Buh-Cuh…
(Homer types his name)
Phonics Frog: Huh-Oh-Muh-Eh-Ur
Homer: That's me! Huh-Oh-Muh-Eh-Ur.
(Presses more buttons)
Phonics Frog: This-Is-Huh-Oh-Muh-Eh-Ur-Dok-tor-Hee-kan-ot-cum-too-urk-too-day.(a.k.a., This is Homer's doctor he cannot come to work today.)
Homer: Uh… I'll be right back. (runs to the phone)
(After Maggie reveals she can play the saxaphone as well as Lisa, Lisa grabs it)
Lisa: Not for babies. (shoves pacifier in Maggie's mouth)
Simon Cowell: (seeing his name in the credits) Now, there's a celebrity!
(As the Gracie Production goes on, the traditional "Shhh")
Simon Cowel: Oh, shhh yourself!
During the end credits, you hear Simon making comments about various members of the production team.
Blackboard Joke: None.
Couch Gag: A dry-cleaning conveyor is suspended above the couch. The conveyor is filled with numerous garment bags. The conveyor begins moving and then stops, with each member of the family in a garment bag, hanging above their respective place on the couch.
Simon Cowell: She's as common as an angry woman in an Ibsen play.
Cowell's revelation that Maggie is only smart because she's watching Lisa is similar to the case of Clever Hans at the turn of the century. Hans was a horse reputed to be able to think. He would answer yes and no questions and add and subtract numbers, answering by tapping a hoof. Oskar Pfungst, a young German psychologist, proved the horse was responding to the nonverbal cues of the questioner--head nods, finger movements, eye twiches, and such--that they weren't aware they gave. So in short, horses can't think. Ibsen was an Icelandic playwright who invented the realistic drama and wrote Lady From the Sea, A Doll's House and Hedda Gabler, which are stark tragedies with female protagonists.
What Ever Happened to Baby Jane
The sequence with the older Lisa and Maggie is a parody of the 1962 film "What Ever Happened to Baby Jane?"
Lisa staying in the Natural History Museum is a reference to the book "The Mixed Up Files of Ms. Basil E. Frankweiler," in which kids ran away from home and lived in the local museum.
The song that is playing right after Lisa runs away is 'Moon River' from the 1961 film "Breakfast at Tiffany's." The scene also parodies a moment in the film where "Fred" is looking for Holly Golightly in New York City.
The title spoofs the title of the 1994 film "Dumb & Dumber" starring Jim Carrey & Jeff Daniels (the title's self-explanatory).