Fighting and capturing the invisible villain in "Hotel Strangeduck."
The ending of "Robot Robbers" is awesome if only because of the sudden twist in its Aesop. In 9 out of 10 cases where the villain mocks the hero by calling him "too soft," the hero learns that may be true, but that's what makes him the good guy. This time, after Flintheart Glomgold tells Scrooge he's gotten soft and afraid to take risks, Scrooge proves Good Is Not Nice when Glomgold needs to hire McDuck Construction to rebuild the city his giant robots destroyed:
Glomgold: How much will that cost?
Scrooge: How much ya got?
Glomgold: Scrooge, you're a low-down, ruthless rat!
The one time this version of Scrooge really resembles the Bad Ass comics' version is when he's wrongfully sent to prison in "Duckman of Aquatraz": The other prisoners challenge him to an arm wrestling match, and he effortlessly beats each one in a second or two, one after another. "Next... next... next..."
Not to mention barely five minutes after he steps foot on the moon, he starts picking fights with a technologically advanced batch of aliens. And is winning single handedly.
Early in the series El Capitan points his shotgun at Scrooge, and Scrooge's response was to give El Capitan quite a glare despite the fact that El Capitan is pressing his Shotgun at Scrooge. That alone is good evidence on how much of a Bad Ass Grandpa Scrooge is.
In a flashback episode where Scrooge told the boys about his rise to fortune, he recounted a time, just after arriving in the U.S., where he was arrested for wearing a skirt in public ("It's a kilt!"). When it came to trial, not only was he found not guilty, but the arresting officer was sentenced to 30 days in a skirt for offending the Judge's own Scottish pride with such a prejudiced charge.
Crashing Scrooge's wedding in "Til Nephews Do Us Part." She tears into Duckburg, shotgun in hands, to break up Scrooge's marriage to a Gold Digger. And you thought EVE was too Trigger Happy...
Her Batman Gambit in "Ducky Mountain High:" Scrooge found gold trees growing on her land adjacent to his and "tricked her" into trading their land because he thought the gold deposit underneath the trees giving them their color must be there, too. It's not until he starts digging that he finds out what Goldie knew all along — he now owns the land with the gold trees, and she now owns the land with the gold! And she rubs it in Scrooge's face while flirting with him!
Scrooge: Why you poker-face prospector! You knew about the trees and the gold all along!
Goldie: Well, who do you think sent you that gold stationary to lure you up here? I've been working on a way to get your land for months. Now I've got a gold deposit, and you've got a lousy bunch of tree stumps.
Scrooge: Oooh... Goldie, you're a dirty deal-maker!
Hypnotizing Gladstone Gander to use his luck to steal Scrooge's Number One Dime in "Dime Enough For Luck" and cursing him with bad luck afterwards! Not only is it incredibly satisfying to see Gladstone suffer for once, but the fact that she was able to pull this off at all makes Magica possibly the only force in the Scrooge McDuck Universe that's stronger than Gladstone's infamous luck! Carl Barks would have loved this episode, seeing one of his favorite characters take down one of his least favorite. Oh, and "Bad luck, old chum!"
Trapping Scrooge in the future, finally getting his Number One Dime, and taking over the world in the alternate future (starting a trend for Disney villainnesses?) in "Duck to the Future."
Huey, Dewey, Louie, and Webby
The triplets defeating Circe in "Home Sweet Homer."
Huey's moment comes in "Pearl of Wisdom," when he destroys a torpedo using only a marble.
Another awesome nephew-related moment: the last five minutes "The Money Vanishes." The Beagle Boys steal Gyro's furniture mover ray and use it to steal Scrooge's entire fortune. When the trio discovers that the Beagles are behind the theft, the crooks try zapping them with the ray and sending them off the face of the Earth. But then thanks to a goof up the nephews wind up getting the ray and the Beagle Boys realize that they are 100% royally screwed.
Dewey: Come on, Beagle Boys! Take my ray!
Webby has one in "Back Out In The Outback" when she, with the help of the animals she's befriended, captures the criminals who have been responsible for the willy wisp attacks.
Scrooge: Webby, how did you ever manage to capture such desperate criminals?
Louie in "Much Ado about Scrooge," where Scrooge, the nephews and the descendants of the Drakespeare Players at Great Written find out William Drakespeare's last play, "MacDuck," is a disgrace to the McDuck name. Filler Brushbill, super-duper door-to-door salesman, though, had been promised half the play's proceeds for his help in getting the play, and on that verdict finds out he'll get nothing for his efforts from Scrooge. In a panic,he takes "MacDuck" in an effort to get something out of it. Louie, though, manages to talk him out of ruining his reputation as "the super-duperdoor-to-door salesman" with a play so awful nobody would ever buy anything from him ever again! Filler comes to his senses long enough to agree, admitting Louie "did a great sales job" on him. Given Louie himself thought of doing door-to-door sales one day, Filler later gives Louie an endorsement at the end.
Launchpad gets a few of these in the episode "Where No Duck Has Gone Before". Huey, Dewey, Louie, Doofus, and Launchpad have gotten stuck in outer space with an egotistical actor who plays a hero in a sci-fi show and thinks he's stillfilming an episode. When the actor realizes they've actually been captured by aliens, he escapes back to Earth, abandoning the others. Launchpad then shows the boys what real heroes do, and saves the day.
The entire second half of "Hero for Hire" is one giant CMOA for Launchpad. The Beagle Boys use him as an unknowing patsy in all their robberies so he'll take the blame, and then they take Doofus hostage so he won't try and clear things up with the police. Launchpad then proceeds to fake his own death, locate the Beagle Boys' house, and saves Doofus while recovering the stolen money.
In the series finale, Scrooge, Launchpad, and Dijon have to return the Golden Goose to a temple, lest it's curse consume the entire planet, and turn everyone and everything to gold. With time running out, and nowhere to land, Scrooge, for once, actually orders Launchpad to crash their plane, which he gladly does...only to execute a perfect, flawless landing for the first, and only, time in the entire series.
That wasn't the first time, he was told to crash the Hindentanic, and the crashing in itself was pretty awesome since the blimp was on fire and in the middle of a meteor shower.
While minor, Launchpad loop-the-looping and making Armstrong's missiles crash into each other.
Fenton Crackshell / Gizmoduck
Fenton Crackshell gets his by defeating the Master Electronic Leader in their counting contest in "Super DuckTales".
And then to add to that, he manages to singlehandedly take on and defeat the planet's entire inhabitants while Scrooge and Launchpad escape, recover the Money Bin, and steal their ship to rendezvous with the pilot and their mutual employer.
Fenton successfully stopping the metal mite invasion, even after losing his Gizmosuit.
Mrs. Beakley gets one in "Down and Out in Duckberg". Scrooge is suffocating on the bottom the ocean. When warned that the waters are infested with sharks, her only reply is "Now they're Beakley-infested waters!" Then she dives off the boat and saves Scrooge almost single-handedly.
Another for Mrs. Beakley is in Cold Ducks. After seeing a giant woolly walrus smash a museum, she proceeds to shout "Hey lardo!" and use a scarf as a bullfighting cape.
Alan Young alone gets one for reprising his role as Scrooge and giving it his all despite his very old age.
Ditto for June Foray (Magica DeSpell), who was 95 at the time.
While Joan Gerber, Hal Smith, and Hamilton Camp could not reprise their roles as Mrs. Beakley, Gyro Gearloose, Flintheart Glomgold, and Fenton Crackshell/Gizmoduck because they all died before the game was made, their replacement actors Wendee Lee (Mrs. Beakley), Chris Edgerly (Gyro), Brian George (Glomgold), and Eric Bauza (Fenton/Gizmoduck) deserve some points for being able to do the voices well enough that one can hardly tell the difference!