In the two-part origin special the ninja first use the Tornado of Creation and end up creating a ferris wheel with the skeletons caged in the gondolas. Nuckal inexplicably has a cone of cotton candy, then Kruncha knocks it out of his hand prompting him to let out a depressed "Aww".
Another Nuckal and Kruncha moment near the beginning: At the skeletons' strip mining site Nuckal finds a ring-shaped rock and thinks it looks like a donut, then tries to take a bite out of it to see if it tastes like one. It doesn't.
After Sensei Wu tells the ninja about the golden weapons, Kai reminds him about his sister. The response from Jay is priceless.
Jay: We're saving a girl? Is she hot? Cole: Jay! Jay: I just want to know what we're getting ourselves into. (To Kai) Does she like blue? Kai: (Death glare) Back off!
In "Home" the ninja flashback to times where Zane acted "weird". In Cole's example, he walked in on Cole on the toilet and mindlessly combed his hair, in Jay's: Jay, Nya, and Zane are watching a movie where a couple break up and Jay and Nya are weeping but Zane laughs like a maniac . In Kai's flashback, Kai is walking to the refrigerator for a late snack. The note Zane leaves is hilarious, "I'm sorry, I've consumed the last of the deli meat...cheese?"
In some versions, Zane is actually STANDING IN the refrigerator eating a sandwich.
During the part of "Can of Worms" where Kai gets inflicted with Venomari spit he sees the Venomari and Constrictai as elves and gingerbread men.
Look! A magic flying rope! We can climb to safety!
When they're saved by Samurai X he mistakes him for Santa Claus.
Look at Sensei's beard! It's moving like snakes! *sticks a dumpling to his cheek*
In "Snakebit" Jay's parents were embarassing Jay through their visit and reveal some of his secrets.
Sensei: Now that they have left, perhaps Jay can teach us the art of kissing pillows.
In "Tick Tock", Zane discovers why his sense of humor is so dry: he's an android (Nindroid?), and his humor switch is turned off. Turning it on results in a singing, dancing Zane, complete with Michigan J. Frog impression.
In "Once Bitten, Twice Shy", Zane accidentally freezes himself, Cole, and Kai in a giant block of ice. His response? "Oops."
On another note, Jay's somewhat dumbfounded face after Nya kisses him can be this.
"The Green Ninja" is chock full of funny:
Garmadon moves in with the ninjas after a Heel-Face Turn / Enemy Mine. He has an interesting lifestyle to say the least, like sunbathing in a thunder storm and filing his teeth with a black dagger. He even refers to Kai as "Mr. Snoopy Pants" at one point (made funnier by him wearing a purple four-armed robe when he says it).
When Garmadon and Lloyd are reunited, we get this exchange.
Jay freaking out throughout the beginning of "Day of the Great Devourer":
We are so hooped!
Jay: Let me make a note of that. Giant snake has itty-bitty weak spot that will be TOTALLY IMPOSSIBLE TO GET AT BECAUSE THE THING IS TOO RIDICULOUSLY HUGE TO DO ANYTHING TO STOP IT!
He also suggests they hide in the Serpentine tombs until the Devourer crisis blows over, stating they'll be without sunlight for months but at least they'll be safe.
In "Pirates vs. Ninja" when the ninja ask how they're going to get around Ninjago City without their vehicles Sensei Wu offers them something he claims will allow them to get around better. They assume it will do something like conjure a portal, but when Cole examines the device it turns out to just be a bus token.
All of the gags that had to do with One-Eyed Pete and his seeing eye parrot.
Lord Garmadon: I told you fools, they're UNSPEAKABLE!
Not to mention him begging the Mega Weapon to work while chasing the Ultimate Dragon.
In "Double Trouble", Lord Garmadon and the Serpentine are trying to devise a new plan to defeat the ninja. A Constrictai suggests they get more pirates and gets thrown off the Black Bounty. A Venomari then suggests they recreate the Great Devourer and is also thrown overboard.
Also, another one suggests making a giant sandwich. When Garmadon asks if it would be a poison sandwich, the snake hopes not because he is hungry. And when another snake brings it up later, Garmadon throws him overboard as well.
Throughout the episode, Cole is obsessed with cake.
When the teachers and ninja are locked in a room, they try to find a lever that'll let them out. The first lever they pull makes the room compact ala A New Hope trash compactor. The second lever not only doesn't stop the shrinking, it adds spikes to the ceiling.
When Cole's dad is eliminated from the race in "Ninjaball Run".
Jay's over the top cry of "WHAT THE HECK IS THAT?!" upon seeing the Stone Samurai in episode 20.
Three words: "Rock, paper, clamp."
Skales' Big "NO!" after the Serpentine are sealed in the Stone Army's storage chamber is broken up by him coughing.
After the ninja regain their powers in "The Island of Darkness", they proceed to kick some Stone Army butt...except Cole, who decides to start dancing on their heads once he traps them in dirt.
Cole: Hee, hee!
In the beginning of "The Island of Darkness", Lloyd learns that he'll become the ultimate spinjitzu master. He responds by laughing and mocking the four ninja with "Jealous?" Afterwards, Lloyd is forced out of a mission to prevent from facing his father prematurely. Jay responds with "Jealous" the same way Lloyd did just a moment ago, laugh included.
"Bequeath, bequeath, bequeath!"
When Garmadon is about to use the Garmatron to launch a dark matter bomb at Ninjago City the ninja stuff General Kozu into the missile silo instead. He ends up getting launched through the window of Dareth's dojo, where his students promptly beat him up.
When the ninja get to evil Ninjago and see it's been taken over, Cole gleefully talks about how he can't wait to see the look on the Overlord's face when he sees they're there. Cue the ninja getting shot at by a gun that shoots pure darkness
Zane: Is that the look you were hoping for? Jay: Zane! *Beat* No...
Jay trying to the tell the guys the moral of the story in "Once Bitten, Twice Shy" and getting shot down by Cole:
Jay: No matter if you're a snake or a samurai, it's important to be yourself— Cole: Yeah, that's cute.
Zane freaking out over his Green Ninja dream and wondering if he's still dreaming until Cole smacks him in the face with a pillow.
Cole: Did that feel like a dream? Zane: *deadpan* No. Thank you for your help.
"That is not a coconut!"
When Cole gets his elemental blade and suit, he does a moonwalk. He's Mi-Cole Jackson!
Jay dressing up as a woman and lying down in front of a train to fool the Samurai into saving him in order to discover "his" identity in "The Snake King."
From the same episode, Sensei getting excited over a Ferris Wheel.
The ninja, completely exhausted after their day jobs:
Cole: My feet! I can't feel my feet!
Kai: There were so many... and they wouldn't stop.
When Garmadon wants to lighten the Dark Bounty's load, he tells the Serpentine to throw off any excess weight. One unlucky snake asks what to throw off. Cue shot to that same snake flailing as he's tossed off the ship, tumbles through the air, and lands in the ocean.
Dareth. That is all.
The newscaster during "Day of the Devourer," "People are advised to run away waving their arms in panic and screaming like little children!"
When Garmadon is confronted with a warm-up period from the Ultimate Weapon,
Garmadon: YOU COULD HAVE WARNED ME THERE WAS A WARM-UP!
Overlord: *flatly* How could I? You were monologuing.
From a sneak preview of the next season, we see that the technology of New Ninjago City... doesn't really like the Ninjas.
Kai getting his foot stuck in an automatic door.
P.I.X.A.L. Asking what Zane's name stands for. He doesn't get it t first and says he stands for honor and other things till Cole points her real question out to him.