* When the Leviathan is attacking the Ulysses, Mrs. Packard sounds the alarm with a monotone, "All hands, abandon ship."
** In the same scene: "[[SkewedPriorities He took his suitcase? Marge, honey. I don't think he's coming back.]]"
** And when Mrs. Packard has to leave because the sub is seconds from annihilation. "I have to call you back. No, no, I'll call you." All in the same monotone.
* This dialogue between Milo and Vinny while loading the sub.
--> '''Vinny:''' Oh, ehh, gunpowder, nitroglycerin, notepads, fuses, wicks, glue, and uhh… [[ArsonMurderAndJaywalking Paperclips.]] Big ones. You know, just, eh, [[BlatantLies office supplies.]]
* When Milo is speaking to Kida in several different languages and she speaks French, Mole excitedly exclaims "She speaks my language!" and promptly whispers something in her ear. Her response? Punching him in the face.
** Kida's face prior to her punching his is amusing.
** Made better when the others immediately take a liking to her as a result.
-->'''Audrey''': Hmm. 'bout time someone hit 'im. I'm just sorry it wasn't ''me''.
** Based on the subtitles, what he had started to ask her was, "[[ShoutOut Voulez-vous]] [[IntercourseWithYou coucher]]..."
* Vinny's advice during the final battle: [[CaptainObvious "Don't get shot!"]]
* The scene with the pillar.
-->'''Milo:''' Will you look at the size of this? It's gotta be half a mile high, at least. It must have taken hundred -- no, ''thousands'' of years to carve this thing.
-->'''Vinny:''' ''(detonates his TNT charges so it falls down over a chasm)'' Hey, look, [[BridgeLogic I made a bridge]]. It only took me, like, what? Ten seconds? Eleven, tops.
** It's the gleeful look on Vinny's face that seals the deal.
* [[FreudianSlip "I know how to swim pretty girl--good! Pretty good, I swim pretty good."]]
** Milo's boxers then inflate after going into the water.
*** Even funnier: if you look closely, you can see Kida trying not to laugh.
** Also funny, is that as a trained linguist he should have known the correct wording was "[[YouMakeMeSic Pretty]] ''[[YouMakeMeSic well]]''". He's so [[DistractedByTheSexy distracted by Kida]] that he forgot ''grammar''.
* The picture of Preston Whitmore and Thaddeus Thatch immediately post-kiss. They're both recoiling, and it looks hilarious. [[TheBet And it's Whitmore's fault.]]
-->'''Mr. Whitmore:''' I said, "Thatch, if you ever actually find that so-called journal, not only will I finance the expedition, [[TemptingFate I'll kiss you full on the mouth]]." Imagine my embarrassment when he found the darn thing.
** Early on, as Helga brings Milo to Whitmore's mansion, she speaks to him like he's a serious, tough guy. Then the next scene reveals that he's the complete opposite: a funny old man who Snarks at nearly every opportunity, even making the above bet.
* When the ''Ulysses'' finally descends into the ocean, for a split-second, you can actually see a man waving at the viewers.
* When Milo starts up one of the flying machines:
-->'''Vinny:''' Hey, Milo, you got somethin' a little more sporty? You know…like a tuna?
** Clearly, [[DeadpanSnarker Vinny]] gets all the best lines. From earlier:
--->'''Vinny:''' We've done a lot of things we're not proud of--robbin' graves, [[DepartmentOfRedundancyDepartment plunderin' tombs]], [[ArsonMurderAndJaywalking double parking]]...But nobody got hurt! ({{Beat}}) Well, maybe somebody got hurt, but nobody we ''knew''..."
--->'''Vinny:''' (upon seeing the sketch of the Leviathan, which resembles a lobster) With something like that, I'd have white wine, I think.
** And then there's when he tricks Milo into thinking he drank nitroglycerin. "Don't move, don't breathe, don't do anything...except pray." "BOOM!" *Mole and Vinny walk away and laugh* And later: "Hey, too bad we don't got some nitroglycerin eh, Milo?"
* Sweet's medical check-up of Milo, ending with him handing Milo two enormous beakers and telling him to fill them up. Milo does a SpitTake on the thermometer in his mouth. "With ''what''?!"
-->'''Sweet:''' (sticking a tongue depressor in Milo's mouth) So, where you from?\\
'''Milo:''' (unintelligible)\\
'''Sweet:''' Really? [[IntelligibleUnintelligible I got family there.]]
* Sweet's way of dealing with Mole after poor Milo sat on the dirt collection: show him soap, and yell as Mole retreats, "Back! Back, foul creature! Back to the pit from whence you came!"
** Sweets rat-tails the poor man!
* Milo getting sick over the side of the ship. "Carrots, why is it always carrots. I didn't even eat carrots."
** It should be noted that his voice actor, Michael J. Fox, is [[TruthInTelevision actually allergic to carrots]].
* Dr. Sweet, telling Milo that he [[YouDontWantToKnow doesn't want to know about Mole's backstory]].
-->"Trust me on this: you don't wanna know. Audrey? Don't tell him. You shouldn't've told me, but you did, and now I'm telling you, you don't wanna know!"
* [[EyeGlasses Kida trying on Milo's glasses.]]
* We are briefly given a shot of Milo and Audrey in an escape pod as Milo nervously chants "it's only a grease trap, it's just like a sink, it's only a grease trap, it's just like a sink..." Just the way Milo's voice sounds when the says the second "sink" gets me every time.
* "Hah! What have you done? England must never merge with France!"
* When the crew realizes they're in a dormant volcano, Sweet asks if it could erupt at any time, but Mole says that it would require "an explosive force of tremendous magnitude." Everyone immediately turns to Vinny, who is tinkering with one of his bombs.
-->'''Vinny''': ''({{Beat}})'' Maybe I should do this later, huh?
** Then when the volcano has awoken:
-->'''Vinny''': ''(while holding a sizzling stick of dynamite)'' Hey, I had ''nothing'' to do with this!
* It was in the midst of a dramatic moment, but there's just something unexpected enough to be amusing when a princess in a Disney movie kicks an enemy ''indelicately'' and then pulls a knife. Now why didn't [[Disney/BeautyAndTheBeast Belle]] ever think of that?
* Milo attempting to drive a truck.
-->'''Milo''':'Course I can drive a truck. Sure, you got your steering and your gas and your brake and, of course, this metal, uh, looking... thing. Okay, so it was a bumper car at Coney Island, but it's the same basic principle.
* The slide show.
-->'''Milo''': The first slide is a depiction of a creature, a creature so frightening that sailors were said to be driven mad by the mere sight of it.
--> ''[a picture of Milo on the beach wearing flippers, a dragon-floaty and a fishing pole is shown while his cat Fluffy plays with the end of the fishing pole]''
-->'''Whilmena Packard''': Hubba, hubba.
-->'''Audrey''': (eye roll) Geeze, I used to take lunch money from guys like this
* Cookie is serving everybody the same brownish, disgusting slop:
-->'''Cookie''': For the appetizer, Caesar salad, escargot, and your Oriental spring rolls.
-->'''Mole''': I wanted the escargot!
-->'''Audrey''': ''[Gives Mole her tray]'' Knock yourself out...
** Later on during the same scene:
-->'''Cookie''': Main course!
-->''-Nobody wants to eat any more-''
-->'''Cookie''': Don't you worry. It'll keep and keep and keep!
-->'''Ms. Packard''': Thank God I lost my sense of taste years ago.
-->''-Everybody dumps their food into the campfire, [[LethalChef which causes a small explosion]]-''
* When Milo is getting ready to interrogate Kida, he first recites what he's going to say to her after seeing her step out in the open. ''However'' just as he's about to talk to her, she sneaks up behind him and tells him [[IronicEcho the exact same thing he was going to say]].
* [[BrutalHonesty "We're all gonna]] ''[[BrutalHonesty die.]]''" ''(flicks cigarette away)''
* Everything Mole does in the sequel.
** When the team gets attacked by the [[EldritchAbomination Kraken]] for the first time, Mole loses his cheese that he was eating which rolls into the water. When the Kraken reveals itself for the first time (in this case showing off its tentacles and roaring), Mole weakly says "Uh, you can have it."
** "*after saving Audrey* You see? You cannot live without me."
* Milo trying to explain a life preserver to Kida.
* "How bout you translate and ''I'll'' wave the gun around!?"
* Post-mass slide into darkness:
-->'''Rourke:''' All right, who's not dead? Sound off.\\
* collective groans from main characters*\\
'''Cookie:''' Dang blasted bugs done bit me on mah sit-upon! Someone's gonna have to suck out this poison! Now don't everybody jump up at once.
* At the museum, all the board members, save for Mr. Harcourt, quickly take cover in different rooms when Milo comes up, and as Mr. Harcourt tries to get into a room, [[ScoobyDoobyDoors we see one of the board members run out of one room to one across from him.]]
* Mrs. Packard stating she sleeps in the nude, then Sweet tossing Milo a sleep mask and explaining "she sleepwalks".
** The very next shot is Vinny wearing a sleep mask, lending credence to Sweet's claim.
* "Attention, tonight's supper will be baked beans, musical program to follow." [[{{beat}} (Beat)]] "Who wrote this?"
** Funny in itself, but also a ParentalBonus; an allusion to the old P.A. gags from the TV series ''MASH.''
* A FreezeFrameBonus: Right before Cookie argues with Helga, a quick look at his wagon shows the writing "TODAY'S SPECIAL: SHUT UP AN' EAT!"
* This exchange when Rourke is taking Crystal!Kida away from Atlantis, causing the water to dry up and the Atlantean crystals to lose their glow.
-->'''Milo:''' We can't let them get away!
-->'''Vinny:''' ''(grabs his arm)'' Wait a second!
--->''[everyone dives for cover as the bridge explodes, leaving the crew trapped on the island with a gaping chasm between them and Rourke]''
-->'''Vinny:''' Okay, now you can go.
* "Whoever took the L from the Motor Pool sign, ha ha, we are all amused."