Chazz telling his new opponent, "Look, kid, you're an obnoxious little punk. And I can respect that..."
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 The Episode with Camula 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 flys 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.
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!
For season three, we turn to Jim for a quick giggle moment in a very dark part of the story. He and O'Brien, along with two new friends just made, arrive at a village that's under attack by Haou's forces. Total Defense Shogun, known as Burgandy, is defending his village from those forces. Jim rushes up declaring that he will help, but Burgandy 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. Burgandy 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 I will say this in just 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 Asuka 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?"
In the same episode, Manjourne annoys Asuka by imagining her as an idol, and then Misawa comments she's probably too old to be an idol like that, only to get hit really hard, while Manjourne got 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's 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 Jessie/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 of 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
Jessie: 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 an Awesome Moment 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 always sticks out in my head. 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: