In Episode 31, while admittedly it happened off-camera (if at all), Serenity convincing the kid that thought he was Ash that he had cancer was pretty awesome.
The ending also applies:
Joey: Let that be a lesson to you—minor characters from season 1 stand no chance in this tournament. That's why I'm gonna take you out, one at a time! Because I'm Joey Wheeler: Card Game Warrior! Weevil: Would you like to see my bunghole? Joey: Okay, Tristan, now you can break his neck. Weevil: (head twisting sharply to the right) AGH! (Weevil falls over. Cut over to Tristan, standing several yards off.) Tristan: (casually) Yeah, I can break necks with my mind.
Episode 32 ending with Marik getting on his motorcycle and tear-assing around Domino City, set to "More than a Feeling".
Grandpa Moto: Shut up, Mokuba— Mokuba: NO, YOU SHUT UP! (Grandpa Moto and Tea look at him in utter shock)
This exchange from Episode 40 is so cold it becomes awesome.
Yami: "Hey, Bakura! Any last words before Slifer toasts your ass?"
Bakura: "I want my mommy..."
Yami: "That'll work."
In Episode 43:
Joey: "Melvin, you son of a bitch. You stay away from Mai, or I'll—"
Melvin: * pulls a lightsaber out of his Millenium Rod* "You really have no clue what you're *** ing with here, do you?"
Joey: "Uh... yeah, I'll just be getting out of the way now."
Melvin: "That's what I thought."
And one for Mai that she didn't get in the original anime; making Melvin forget about Mr. Tweetums.
Ishizu Ishtar shuts Kaiba up mid-rant about how awesome he is to turn his entire strategy on its head. Kaiba, generally the calmest character, flips out and drops a huge F-bomb extended over several scenes.
Note that we're talking about the same character who maybe 30 seconds earlier told Ishizu to, and I quote, "Put up your f* cking dukes, bitch! 'Cause you're going down, Kaiba Corp-style!"
The only uncensored f-bomb in the series, at that. Not counting the "I'm on a Blimp" video.
In many ways, the climax of Episode 36 comes surprisingly close to being played straight. All things considered, it actually kind of works.
Joey's speech from Episode 50, after being accused by Johnson of Team 4Kids of copyright infringement:
Joey: Yeah, I have a closing statement. Maybe we have committed copyright infringement. But you gotta know we've done everything in our power to support the Yu-Gi-Oh franchise! And if it weren't for us, I don't think the show would be nearly as strong as it is right now!
Johnson: And where is your evidence of such?
Joey: Look around, Johnson! There are more Yu-Gi-Oh fans now than ever before! And the more you try to stifle our creativity, the more we'll try to express our love for a show that's about more than children's card games! It's about fighting for what you believe in, and I believe in this show and its fans now more than ever! Because they believe in me!
Yugi: This is so meta.
Joey: Flame Swordsman! Use the strength given to me by the Yu-Gi-Oh fanbase to wipe out his life points!
Flame Swordsman: My name... is... FRANK!! [commences to pwn Johnson's Deck Master]
Ironman playing when Mecha Nezbit first appears.
Tristan's pre-death speech (doubles as a Crowning Moment of Funny at points)
Tristan: It's okay Serenity, I lived my life as a side character, fit only for spouting mindless quips and catchphrases. But now, I get to die the way I always wanted, falling, screaming like a girl into a pit of boiling hot lava, flesh being seared from my bones. If I do survive, I'd probably be unrecognizable. But if I do die, It'll be as a main character.
Episode 53: By this point, its almost time for the big 5's final duel, but due to a little bit of editing, Tea's currently possessed by the Penguin-obsessed member of The Big 5. However, in the pre-opening part of the episode, after witnessing the guy fail at being Tea, the part of Marik that possessed Tea speaks up and, after a quick conversation, literally kicks the guy out. Let me say that again. Marik's spirit, without the rod, managed to kick out another spirit who had taken over a body he only possess occasionally.
Melvin tells Ishizu that he's sending everyone to the shadow realm, saving her for last. Why? Because shut up. His cold delivery sells it.
The We Will Rock You parody in Episode 59. Plus Yami winning against Kaiba for the gajillionth time.
Kaiba gets one in episode 60: when confronted on his anger by Mokuba and the notion he considers the others friends, he calls Duke, Joey, and Tristan out on their failings in spectacular fashion.
Admit it, the parody opening in Doctor Who style for the crossover abridge movie was freaking awesome!
In the movie, we have Yami Yugi doing what he does best to take down Paradox...screwing the rules.
Yami: So stand back y'all, cause it's time for a real main character to take the field.
Paradox: Oh pwease, you may be the King of Games in your timewine, but where I come from duel monsters has evolved far beyond your understanding. Compared to me you are just a learner.
Yami: That may be the case in your timeline Paradox, but then we're not in your timeline, are we?
Yami: And where I come from, duel monsters is still a broken, exploitable mess of a game. And I'm about to exploit the hell out of it! (summons Dark Magician and Dark Magician With Big Boobies and destroys his Malefic Paradox Dragon)
Yami: I believe the appropriate phrase is, 'Boo-yah'.
In the maybe-canon spinoff fanfic Marik & Bakura Go To Censored Town, Ryou Bakura, of ALL PEOPLE, has one of these, when he convinces Florence to go back and apologise to Marik, making Florence realise that Marik is the only real friend that he has. To do this, he actually takes control of one of his arms so that he can force Florence to look at a photo he had of Marik. Considering that he hadn't even been mentioned in the fic up to that point, and how he's been pretty much ignored for most of the Abridged series, it was pretty awesome.
Ryou: If I were in your place, I would rather die than lose any of my friends. Especially one that means as much to you as him.
In the first episode of Season Zero, the way Yami convinces Yugi to finish the Millenium Puzzle, takes over his body (Which was also kind of creepy, but in a cool way), and then kills Ushio in, what one would say, the most epic moment in the show.
Yami: Garbage Day!
Ushio: Yugi! What are you doing?
Yami: Ushio, baby! How's it hanging? Get it? 'Cause your gonna Die! Hehe...
Yami: Guess you had be there...
Ushio: So... are you gonna give me the money now?
Yami: Tell you what... (Slides down building as rock plays in the background, sliding playing cards along the way, stops right in front of Ushio, hanging by a rope) Hi.
Yami: Wanna Play a game?
Ushio: ..What kinda game?
Yami: Whoever dies first loses!
Yami:(Holds up a playing card) Look, the Queen of Spades!
Ushio: ...What does that d-
Yami: You lose! (Lets go of rope holding Ushio, dropping him into a lake of man-eating Worms) Hope ya like Man-eating Worms!
Ushio: huh, I wonder what he meant by tha- (Notices Giant Worms) OH MY GOD THAT IS WHAT HE MEANT BY THAT!
During the absolutely hilarious "Michael Bay's Yu-Gi-Oh", Yami appears, criticizes all of the ridiculousness around him, points out plot holes, and pretty much explains WHY Michael Bay movies don't work. Then asks why we can't have a loyal adaptation of a much-loved show from Hollywood. Awesome.