In the opening sequence, there's a brief montage of the entire main cast hula dancing. Why is this "funny" instead of simply "cute?" Because we truly mean the entire main cast, up to and including Jumba, Hämsterviel, Gantu, and Cobra Bubbles (who even kept his Men in Black suit on and just put on a hula skirt over it).
The fact that when they end up being chased by Phantasmo, the ghostly experiment possesses... an animatronic toucan. Of all the things to attack someone with, it goes with a Hawaiian Toucan Sam.
Stitch unsuccessfully attempting to get in on Lilo's thought process.
Lilo: You look like a hairy hairball... and you seem to like to eat hair... and you're made of hair... so I'm going to call you... Stitch: Hairy! Lilo(as though the very idea is ridiculous): No! "Clip"! Stitch: Huh?
Even funnier when you consider Lilo is responsible for such past gems as Finder, Nappifier, and Hotcold. She was even going to name Morpholomew, "Changer", which Trixie convinced her not to go with.
When Clip evades Gantu into a bus, he goes into a big Badass Boast about how she will not escape him - complete with lightning - only to notice some kids looking at him and, slightly embarrassed, simply goes, "I mean, I, uh, missed my bus".
Jumba gets very happy when his hair suddenly grows back (as a massive afro). He makes the whole planet shake!
The fears, aside from Nani's nightmare, are kinda humorous like Jumba being afraid of his ex-wife, Pleakley being afraid of his mother, Mertle and her posse being scared of Lilo. Yeah... they have some rather odd fears.
Gantu fails to realize the concept of a sandcastle.
Gantu(looking up at Stitch's sand-made fortress): Open up! I'm here for the abomination! Lilo: Go away, I like abominations. (she, Stitch and Cannonball blow raspberries) Gantu: (facepalms) I'll have to devise an assault plan for this fortified defense structure. (leans against it, his hand goes through wall) This is just made out of loosely-compressed silicones.
When Lilo tells Jumba and Pleakley about Mertle's sand sculptor idea, they unintentionally agree that it is better than Lilo's idea.
The Never-Ending Dance that Jumba and Pleakley end up going into. Seriously, they dress up in Disco garb and everything and even sing along to a very odd song.
David and Lilo having a rather childish talk about that results in Stitch eating some turtle wax.
Nobody wins around Splodyhead. Seriously, it's mostly Epic Fail when dealing with it while stuck on the island.
Gantu gets hypnotized and 625 and Hämsterviel taking advantage of this by making Gantu do ridiculous things.
Every time Fibber beeps. Seriously, the timing is glorious with each one.
Pleakley perking up when Jumba comes out in disguise as the bride. Rather funny reaction honestly.
Mrs. Pleakley: Goodbye son. Try to wear men's clothes more often.
Pleakley: I will! (Fibber beeps as Pleakley gives a flat look in response.)
The revelation that Pleakley's first name is Wendy. Nani even finds it funny.
When Tank first shows up:
Tour Guide: Don't worry it's just a wild pig. It's likely scared that people are in its habitat. Tourist: That pig just ate a car... (shows that Tank did just that)
Stitch getting very sick of the Bard quickly, smashing his guitar when he finally snaps.
This line in "The Asteroid", after our heroes discover an old hermit on the asteroid, while on a mission to destroy it to prevent it from colliding with Earth. The line isn't just hilariously ironic, it's made even funnier by how nonchalant and blunt Jumba is about it.
Jumba: (cheerfully) Hello, we come in peace to blow up your home.
An experiment's one true place is being a Christmas ornament... and it ends up getting many aliens to come to see where the light is coming from.
Lilo and Stitch + Time Traveling Surf Board = Hilarity Ensues. Highlights include:
At the hospital, Lilo, Stitch, and Pleakley are attacked by Gantu, leading into this:
Lilo: Whoa, whoa, whoa-whoa-whoa. Let's be rational here. I think that there's a way everyone can be happy. And that's if we just... calmly... RUN! (She, Pleakley, and Stitch run away) Gantu: How does that make me happy?
Later, when Pleakley is in danger of exploding, Jumba's only concern is that it might be messy. His solution: getting a big towel.
Whenever someone is spiked, they get 99% sillier. This leads to goofy expressions, silly answers at the trivia contest and mindset of silliness. This especially works on Stitch, who acts overly silly with this effect on him.
Everyone going nuts over Frenchfry's cooking... If not for the Nightmare Fuel with the titular experiment that is, though hearing his overly French accent is still kinda funny.
A lot of characters get switched up; Hämsterviel and Gantu, Lilo and Stitch, etc. It's funny given that they kept their voices.
Stitch!Lilo's blue-white mohawk. Just... wow...
Rainbow Stitch. That is all.
Most of "Shoe" is funny, thanks to the horrible bad luck the titular experiment wreaks upon the entire cast: the whole thing is Amusing Injuries incarnate. Special mention goes to the scene where Lilo is trying to figure out how to help Shoe, while Stitch watches from the windowsill - by the end of the scene, Stitch has been knocked on the head, fallen out of the window and had his fingers smashed upon trying to climb back in. The best part is the final battle with Gantu, however, which quickly turns into a game of "how bad can their luck possibly get?" High points include Gantu being strapped to a hot air balloon and floating in front of a skeet shooting competition, and a random spurt of lava forming at Stitch's feet out of nowhere.
When 625 tries to reveal one other detail about Shoe, Gantu tells him, "Quiet! I do not want to hear anymore about 113!" It turns into a Brick Joke later on when 625 finally reveals that Shoe is also a good-luck experiment and Gantu asks him why he didn't tell him earlier and 625 reveals that he got their whole conversation on tape, which leads into this:
Gantu on tape: Quiet! I do not want to hear anymore about 113! Gantu: But- Gantu on tape: But nothing! Go make a sandwich! Gantu(getting angry): You can't talk to me like that! Gantu on tape: Yeah? What are you gonna do about it, trog? Gantu(takes out blaster and aims it at the tape recorder): Insolent device! Silence! Gantu on tape: I'm not listening! Na, na, na, na-na-na! (Gantu blasts it to pieces)
While Nani is talking to the entire family, Stitch just wanders off while her back is turned and eats one of their potted plants. Cut to Lilo giving him a Death Glare. A few seconds later, Lilo is talking to Nani again and Stitch just quietly spits the plant into the pot.
Retro turns a squirrel into a prehistoric rodent, making a surprise Jump Scare when it jumps into the Dune Buggy, but Pleakley is just curious.
Spud putting one over on Gantu and having Morpholomew turn him into a rabbit.
Lilo thinking Jake is crazy for believing in magical creatures. Lilo is thinking this; Miss 'My-Family-Adopted-Aliens' herself!
Under Spats' Hate Plague, Jumba harasses a hotel critic with a full-blown chicken dance.
Penny seems to notice something is very off when she first meets Lilo and Stitch, making her one of the first characters to question the mentality of the series.