Chazz telling his new opponent, "Look, kid, you're an obnoxious little punk. And I can respect that..."
One episode has Jaden scare Syrus awake with his dream said of being in a duel, leading to this gem.
Syrus: Why cant he ever dream in defence mode?
The entire Maiden in Love episode (in any language). From Blair/Rei screaming and hiding her face when Jaden/Judai starts taking off his shirt, to Zane's/Ryou's absolutely useless social skills and inability to understand that a girl has a crush on him, to Blair/Rei switching her object of affection at the end of the episode and Jaden's resulting panic...
During the duel, Avian/Featherman and Sparkman are put under her Maiden in Love's Monster Effect... until Jaden/Judai breaks them out of it with Burstinatrix/Burst Lady and Burst Return. Cue their realizing it:
Avian: What was I thinking? I didn't want to get married!
Sparkman: Oh boy... Sparkwoman's never going to forgive me!
Burstinatrix: How about you two guys get over here right now, or I'm telling the entire deck!?
There's at least one per season. Season one: Jaden is still in the infirmary after his previous duel, and everyone is standing around discussing what to do since Camula just defeated Crowler. Jaden tries to get up and say that he'll take care of her, but Chazz reminds him that he can barely stand, casually pulls the sheet over him, and to further emphasize that Jaden is in no condition to duel, Jaden cannot get out from under the sheet! Then for extra giggle points, Chazz tells him to quiet down, and Jaden meekly says, "Okay," and does.
During Camula' debut episode she sends her bats out to spy on The Duelists. When one is spying on Banner he's in his room with several garlics hanging and charms laid across the room. The bat sweatdrops as it watches him swing a stick in fear claiming he knows all Vampire tricks since he's seen every horror movie and the bat flies off.
A quite amusing gag occurs when Jaden's preparing to duel Kagemaru. Chazz is struggling to get out of the crater he's landed in, and does so just in time to have Jaden's backpack chucked at his face, knocking him back into the crater. Jaden takes out his duel disk, and chucks the bag back, proceeding to hit poor Chazz in the back of the noggin again as he gets back up.
One of the cards that Chazz salvages from the reject well in episode 35 happens to be Relinquished. Evidently, some idiot student saw fit to throw away Pegasus's ace monster for apparently being too weak.
The entire episode 42. Especially the battle against Dark Magician Girl. Here are some notable mentions:
Syrus/Sho intends to ask Alexis/Asuka to be the Dark Magician Girl. Unfortunately, the outfit has already been taken by Dorothy/Tomoe. Cue to a bit of dress ripping.
Atticus/Fubuki taking pictures of Alexis/Asuka as one of the Harpy Lady. Atticus mention he wants to sent it to their parents and relatives but Fubuki wants to use it to sell it to her fan club. Cue to her chasing him.
The entire crowd booing on Jaden during the match against Dark Magician Girl. Cue to him and his Steam Healer monster sweat dropping.
Episode 56 has some:
When Syrus is hiding under his blankets, he lists the stuff he needs to last a week. One of them is a teddy bear he named "Mr. Fuzzy Bear". This leads to Hassleberry saying, "I do not even want to ask."
This little conversation between Syrus and Bastion:
Bastion: It's time to get your yellow on. Ready?
Syrus: Uh, that only works when Jaden says it.
Bastion: Okay fine.
The second season moment also involves Jaden, while he's wandering around the island trying to find his way to the school building. There is a sign that clearly points the way. The buildings are visible beyond the sign. Jaden cheerfully stalks off in the entirely wrong direction. The sign sweat drops.
A few seconds later, it face faults, it's utterly hilarious!
While Aster defeating Jaden is not really funny, the way his monster does is. Aster's Destiny HERO Dreadmaster takes out Jaden's Elemental HERO Thunder Giant...with a downwards slap.
For season three, we turn to Jim for a quick giggle moment in a very dark part of the story. He and Axel Brodie, along with two new friends just made, arrive at a village that's under attack by The Supreme King's forces. Total Defense Shogun, known as Burgundy, is defending his village from those forces. Jim rushes up declaring that he will help, but Burgundy takes this the entirely wrong way, believes that Jim works for Haou, and brings his sword smashing down on Jim's head, just as the old man Jim was with tells him that this is a friend. Burgundy gets the most amazing WTF look on his face and is all "I hit an ally?" just as Jim goes "ouch" and falls over unconscious.
Season four, we're back with Jaden, and two words: Pharaoh's fleas.
Three more words: Daitokuji-sensei. Toilet.
The dub gets major points for never shying away from the most obvious humor at Crowler's expense:
The above scene is topped off when said monster attacks Alexis with its ATK back to normal. The monsters chosen method of attack? Smacking her in the back of the head. Dub Alexis tops it off by asking "What's your problem?"
Later on in the Duel, Alexis destroys the costume. Cue "Oh, Crap!" Smile from the monster wearing it as the costume disappears out from right underneath it.
In the same episode, Chazz annoys Alexis by imagining her as an idol, and then Misawa comments she can't sing. Alexis responds by flooring him with an Armor-Piercing Slap, while Chazz gets off scot-free.
In third season dub, Ojama Yellow's voice dropping several octaves when he greets a trio of female duel spirits.
An early one: Alexis being called the Obelisk Blue Fairy. Syrus immediately pictures Obelisk with fairy wings.
From the Manga: Bastion duels Jaden so he can get Alexis' number. When Jaden just offers to give it to him, Bastion says that his pride prevents it leading Syrus to point out that he's still not proud enough to just ask her himself.
After Aster explains Duel Spirits in the dub.
Hassleberry: Duel Spirits? What kind of fool do you take me for?
Aster: I don't think you want me to answer that, Hassleberry.
Bonapart sums up Jesse/Johan perfectly in the dub:
Crowler: He seems familiar.
Bonapart: That's because he's Jaden with a southern accent.
About Professor Viper after he gives off an Evil Laugh.
Syrus: Something's not right about him.
Hassleberry: What gave him away? The creepy laugh or the evil music?
After Hassleberry returns from his primitive state in the dub
Jesse: I don't know what's worse, a guy who thinks he's a dinosaur or a guy who thinks he's an obnoxious drill sergeant.
Adrian Gecko: I wonder why everyone thinks out loud at this school.
Professor Viper: "Can't I plot evil in peace?"
O'Brien gets one that also doubles as a Moment of Awesome in his duel with the Mask of Laughter. After MoL spends a moment laughing to himself about how foolish O'Brien was not to finish him off last turn (instead leaving him with 1000 Life Points) and going into detail about how he'll win this turn, he draws his card...only to see his opponent walking away. With an activated trap card, which he then reads to himself.
Yugioh GX Tag Force 2, while not in canon with the anime, does have a genuinely funny moment at the end of Aster's story. After Aster comments that Jaden might find it hard to go pro with his current scores in the academy, Jaden goes a little study nuts, quickly going to ask Bastion for his study tips while the story ties itself up. The funny part is when Jaden decides that it'd be faster to learn from a pro, namely Aster, quickly and pretty much forcing him to help and comes up with a funny line... and given Aster's not so good AI, this makes up for that.
Aster: <Player's name>! Stop laughing and help me would you!?
For those of you wondering, picture it in your head, Jaden is dragging Aster off forcibly by his arm to help Jaden study... and you, his tag partner, just stand back and laugh at him.
When Jaden is dueling the Light of Destruction-possessed Chazz, and the Ojamas eventually betray Jaden.
Hasseleberry: Never trust three mutants in bikini briefs.
When Syrus brings Jaden a bucket of drinking water in one episode and Jaden proceeds to dump it all over himself, an annoyed Syrus gives us this gem:
While she may be a very despicable villain, Camula has a funny line in her duel against Zane after he explains how he has the ultimate attack and defense with Cyber Laser Dragon and Cyber Barrier Dragon.
This exchange from Season 1 of the dub. Several students have gone missing, so the gang go looking for them, only to find them all working on building a gladiator's colosseum. Then they realize Crowler has joined in on the effort.
Syrus: What are you doing!?
Crowler: A man's work!
Banner: A man's work? My, they must have been running very short on men...
After being assigned to write a paper after winning the duel against the Paradox Brothers:
A moment from the first season that shows us just how seriously Duel Monsters is taken: An entire armed military unit shows up to the school in Episode 4 just to deliver a case of rare cards.
Many moments and exchanges in the duel between Alexis and Atticus in Season 2.
Alexis: Laugh it up, bro...'cause I'm about have the last laugh!
When Alexis comes to stay in the Slifer dorm, Chazz offers his completely-renovated dorm that looks like a suite. There's the following line in the dub as he gives the tour:
Jaden: A spa with a waterfall? Don't you think that's kinda...overkill?
Syrus: Oh, we passed 'overkill' somewhere between the bowling alley in the basement and the three-ring circus in the living room.
From the dub when Axel confronts the Supreme King in his castle:
The Supreme King: It's you!? I didn't think you'd ever stop running.
Dimitri, the guy who stole Yugi's deck and started imitating him, especially the English version's over the top imitation ofDan Green. When he uses Kuriboh, he starts talking to it like it was an old friend and "reminiscing" about some of Yugi's adventures. The Kuriboh Sweat Drops.
Even better is the reactions from the others:
Syrus: Battle City? This guy's batty.
Chumley: (Giving a nervous smile) Just smile and nod, smile and nod.
During Aster and Zane's duel, Aster fuses Avian and Burstinatrix to summon Phoenix Enforcer. Syrus asks why Phoenix Enforcer was created instead of Flame Wingman. Everyone else explains that if a duelist fuses Avian and Burstinatrix, they can choose between Flame Wingman or Phoenix Enforcer. Jaden's reaction is basically "I didn't know I could do that! Awesome!". Everyone except Jaden and Syrus face faults and Chazz is understandably not happy that Jaden didn't realize this considering that Jaden uses Elemental Heroes and defeated him twice before.
During Chazz and Bastion's duel in season 2, the Ojama Brothers root for Bastion in hopes that by losing the duel, Chazz will turn back to normal. Their attempts at cheering on Bastion are both heartwarming and funny. Chazz then plays a card that sends the Ojamas to the graveyard to reduce Bastion's life points by firing them out of a cannon.
Also Heartwarming, in the penultimate episode, Crowler breaks down crying because he doesn't want them to graduate and leave him, and is dragged off. Then Kenzan breaks down giving the student speech and is also dragged off, while Shepherd looks annoyed both times.
One of the episodes had Professor Banner and the kids out in the woods. The dub gave us this little gem:
Dub Amber Mammoth in general, due to his hilariously bad Arnie accent.
Although Karen can be scary, in general a huge crocodile being carried around in a backpack is hilarious.
Another Ojama moment from Chazz's Duel against his brother. After wiping his opponent's field with Ojama Delta Hurricane, the Ojama brothers proclaim that Manjoume Thunder is invincible with them around. Then Chazz drops a Spell...
Yellow: "What's this butt-in of a card?"
Green: "'Thunder Crash'?"
Black: (reading the card) "Hmm... 'Destroy all monsters on your field. For each monster destroyed, inflict 300 points of damage to your opponent.'"
The Season 1 dub gives Syrus a hilarious What an Idiot moment when he tries to raft out into the ocean so as to escape the upcoming tag duel with the Paradox Brothers. He can't swim here. When Jaden stops him, he asks Syrus the obvious question:
The Shadow Riders at least ATTEMPT to be scary/intimidating/frightening... except for Don Zaloog. Kinda hard to be scary when the voice actor decided to go with "Christopher Walken" as the voice.
There is something darkly entertaining about Edo/Aster pretending to be a harmless servant to lure the Supreme King's goblin minions to their deaths. Not to mention the screech of terror when one of the minions in question realizes he's locked in a room with HellKaiser. And Edo's snarky reveal that he and Kaiser are the "dark hero" group, so they're not actually going to let the goblins go after getting their information.
In the dub of Season 3, when Zane, Aster, and Axel need to disguise themselves as the Supreme King's soldiers to get into his stronghold.
Zane: I just hope they have my size. Aster: All these fiends are tall and thuggish. You'll be fine.
In the dub of "Chazz-anova", upon finding out that her brother ships her with Chazz, Alexis thinks: "Sometimes I wish he was still in a coma." And then Zaneface-palms and asks if anyone is up for just tackling him.
In episode 23, Jaden is trying to decide which cards to keep in his deck for the upcoming duel against North Academy. His friends try to help him, asking him to use some of their cards in his deck and end up pestering him. He runs off declaring that the only way to look over his deck is to be alone and his friends chase him, saying he cant be alone by himself and want to help him be alone.
He is weirded out by Belowskis laid-back attitude and how it is affecting his friends. They all fall asleep at the end of the episode and he tries to wake them up, saying he will use their cards, before realizing that Belowski was right, the clouds really do look like duel monsters.
The season 2 dubbing of Homecoming Duel has Jaden happily tell everyone that he's returned from space from a beach full of talking dolphins and a volcano with a talking bug. It's the way that Jaden excitedly talks about where he was and what he's been doing that causes his friends to think he really needs some sleep while Aster thinks he's full blown insane. This is honestly topped with Alexis staring at him with a 'WTF' expression when he's talking about it, given she's standing right next to him during that moment.
Manjoume's "investigation" scene in episode 39, also counts as a Moment of Awesome for him.
There's something inherently funny of the way Dark Zane uses Power Wall. Since it causes him to mill a good chunk of his deck to mitigate damage, the anime has him physically throw his deck away to stop a big hit.
During Jaden's first duel with Nightshroud possessing Atticus, Zane, Bastion, and Chazz get a My Significance Sense Is Tingling feeling from their Spirit Keys and investigate. Cut to Crowler happily sleeping and oblivious to his Key's warning.
T-Bone, the light rider. For some reason, the dub decided to make him a wannabe rapper, which leads to some hilarious lines.
T-Bone: Yeah, I'm down. But we be illin, homeboy!
Jaden: I have no idea what he just said.
T-Bone, after his partner was turned into a card.: My homie!