Grandpa when the police are searching Stanley's room:
Grandpa: You don't have to answer that! We have the right to remain silent! Officer: Wouldn't that be nice?
The judge at Stanley's trial initially asks for "Stanley Yelnats" to rise, resulting in all three living generations of Stanleys standing up. After he specifies Stanley Yelnats the Fourth, Mrs. Yelnats pushes Stanley II and Stanley III to sit down.
When Stanley arrives at the camp, he's not too happy to be assigned a cot that previously belonged to someone nicknamed "Barf Bag".
Magnet: This was Barf Bag's bed. (shot of mattress stain) Mr. Pendanski: (off screen) Keep your bed clean!
When Stanley tells the D-Tent boys he was convicted for stealing a pair of shoes, they all laugh:
Squid: From a store or were they on someone's feet? Zig-Zag: Or maybe he killed the guy first. (nudges Stanley) Just left out that little detail, huh?
Mr. Sir's obsession with talking about how Camp Green Lake "isn't a girl scout camp". Becomes a Brick Joke when Camp Green Lake was converted to a girl scout camp at the end.
From the movie, when Stanley finds the fossils, the other boys gather round to have a look, and Armpit reveals a hidden side of himself and squees in an excited voice, "Look at the little fishies! Awww...!" And then, as the others give him weird looks, he deepens his voice and says in an overly casual tone: "I mean, you know, see, it look like those cave pictures, man."
Magnet was caught trying to steal a puppy, and says that he would have gotten away "until my pocket started barking". Even Zero is seen smirking at this.
When Mr. Pendanski asks Stanley whose fault it is that Stanley is at Camp Green Lake (obviously intending An Aesop about personal responsibility) and Stanley responds confidently, "My no-good dirty rotten pig-stealing great-great-grandfather!" The other boys even find it hilarious.
During a montage in which Stanley becomes accepted by the rest of the campers in the movie, Armpit lifts up his arms, causing everyone to run away from the stink. Trust us, it's funnier than it sounds.
When Armpit tries to give the warden a knob he found and gets his weekly shower tokens taken away, who's more upset about this? His cabin mates. Their dismayed groan at his shower tokens being taken away is the funniest part.
Squid: Man, you sleepin' outside!
"Once upon a time, there was a magical place where it never rained." (Long, tense pause) "The end."
Squid's deadpan reaction: "I don't get it."
The fact that Mr. Sir pronounces "the" with a hard e ("thuh end"). It's the one time Jon Voight's faux Texan accent is exaggerated for comedy.
Mr. Pendanski: D-I-G, what does that spell? Zero: (knocks Pendanski in the face with his shovel) Dig! (runs away)
The entire scene when Stanley steals the truck. The whoops from Stanley, Mr. Sir holding onto the truck as Stanley drives it, and then him falling into a hole, followed by Stanley crashing it.
"Whoo! Bye-bye, Camp G-" *CRASH*
"Yeah, keep going! There ain't gonna be no Yelnats the Fifth!"
The campers talking about Stanley and Zero's escape:
Magnet: Maybe he found Zero. Maybe they're still alive. X-Ray: Yeah, maybe the Easter Bunny and the Tooth Fairy are alive too. Squid: Yeah. Maybe my mom'll quit drinking and my dad'll come home. Twitch: Man, when Caveman stole drive that truck? Zig-Zag: (fist bumps him) Yeah, that was awesome. Armpit: Yeah, man. Caveman did have style.
Yelnats the 3rd, correctly thinking he's finally gotten his foot odor remedy to work, tentatively approaches his moody looking wife as she's eating dinner and sheepishly asks "Honey... please smell the shoe." Henry Winkler's delivery, which sounds like a little kid afraid to tell his mother bad news, makes it hysterical.
When Stanley's lawyer walks to her car the first time after arguing with The Warden, she mockingly says:
"Excuse me!"
When the D-Tent boys see her car driving to the camp:
Twitch: Ooh. Jaguar, that's a nice car. Magnet: Don't even think about it, Twitch.
This exchange:
The Warden: You'll do as I say. *walks out* Mr. Pendanski: What did she say? Mr. Sir: Not much. Mr. Pendanski: Then what do we do? Mr. Sir: You'll do as I say. *walks out* Mr. Pendanski: But you didn't say anything either!
Both the timing and the way the lines are delivered makes the moment totally priceless.
Young Warden: I'm tired of this, grandpa! Trout Walker: That's TOO DAMN BAD! You keep digging! Young Warden: Well, excuse me.
Mr. Sir actually says Oh, Crap! when the Texas officer recognizes him.
Right after that:
The Warden: I had no knowledge about this. Mr. Sir: Oh, yeah. Just like you didn't know Pendanski was no doctor, neither. Campers (laughing): What?!! (all the campers laugh)
Zig-Zag: Say, I didn't know Marion was a man's name. Mr. Sir: It ain't.
Stanley telling The Warden "Excuse me?" after she begs him to let her see the inside of the chest.
At the end of the movie we have a particularly silly Funny Background Event; Twitch, a hyperactive boy who got his name because he twitches whenever he sees or hears about a cool car (and indeed, was arrested for trying to steal one) had replaced Zero and Stanley after they left. At the end of the movie, when Stanley is leaving in a limo, you can see Twitch running after the limo excitedly before Squid holds him back.
The statue of Poseidon seen at the end of the film is holding a shovel instead of a trident.
The cast's commentary with Shia LaBeouf (Stanley), Khleo Thomas (Zero), Max Kasch (Zigzag) and Jake M. Smith (Squid) on the movie is actually really funny. Just some of the highlights include teasing one another for farting, calling Eartha Kitt the "sexiest elderly woman" and Khleo Thomas (Zero) still wanting to see her in her Catwoman suit, and threatening to boycott the movie for animal abuse when we see Mary Lou lying dead from a gunshot.
The blooper reel features an D-tent boys cast interview segment with Max Kasch (Zigzag) giving a shout-out to someone named Briana "whom he loves more than anything". The boys all "aww" over that, except Byron Cotton (Armpit) who does a confused double-take to the camera and asks "Who's Briana?"
