Upon beating each of the Koopalings' fortresses, a humorous cutscene is shown of Mario destroying the fortress he's just spent hell getting through. Normally he just blows it up, but after beating Larry's fortress (the seventh and final fortress), Mario picks the fortress out of the ground and drop-kicks it. No wonder we didn't hear from the Koopalings for so long... note Actually, their last appearance would be in Yoshi's Safari, but that's another story...
Fortress #2 is also awesomely destroyed, namely by Mario simply repeatedly kicking it until it crumbles to the ground.
After finishing the Sunken Ship (itself a Call-Back to the airships of Super Mario 3 and, apparently, the ship used by Bowser and the Koopalings to get to Dinosaur Land), the entire screen starts to shake while a unique fanfare plays and the entrance to the Valley of Bowser emerges from the depths of the ocean.
Bowser's entrance in this game. To put this into perspective, his firstconfrontations with Mario were a bit of an anticlimax. Come to this boss, and for the first time in his long career, Bowser drops the act and introduces the Koopa Clown Car, which itself makes a grand entrance by slowly entering the screen until it's in full view, and Bowser pokes his head out in all the game's 16 bit glory. And then came the fight itself. This was when Bowser first earned his mantle as the King of the Koopas, and he hasn't let that title go ever since.
In "Fire Sale", he faces his fear of water to save his friends and Mama Fireplant from Kootie Pie's Ice Palace mere seconds before it collapses.
He also overcomes his fear of ghosts in "Ghosts 'R' Us" to save his friends from Wizardheimer's haunted house.
Two in "A Little Learning":
When Hip and Hop tease Oogtar, Yoshi pulls the stool Hip is standing on, causing him to fall face first into his volcano project.
Also when the giant Piranha Plant eats King Koopa, Hip and Hop, Yoshi boldly prevents them from going any further by swallowing the plant (and its "contents") whole.
"Mama Luigi" is one entire episode of awesome for Baby Yoshi. Between eating everything in sight (including Mario temporarily), destroying Koopa's Castle, and pretty much saving the Princess without much effort from Mario and Luigi, yeah, Luigi's story about Yoshi is awesome.
Also, with all the goofy dialogue in the episode, the line from King Koopa "I can build another castle, but you can't build another princess" actually sounds pretty cool.
After being mocked previously by Mario, who calls him "Mama? Mama Luigi?! Ahahaha!", Luigi later proudly declares "That's Mama Luigi to you, Mario!"
The fight scene between Mario and King Koopa in "Send in the Clown" where Koopa uses his Koopa Clown Car with the Princess in tow, complete with a remix of the final boss music from the game.
Koopa even has a moment in "King Scoopa Koopa" when he absconds with the money he scammed from the cave people after his restaurant is shut down.
After putting up with Kootie Pie's abuse in "Fire Sale", a Koopa Troopa minion refuses to help her when she's stuck in a block of ice.
While trying to modernize the cavemen backfires mostly, "The Yoshi Shuffle" give viewers an exception; Mario and Luigi were teaching some cavemen football to help them learn teamwork. At the end of the episode, when Mario and Yoshi are escaping Koopa's Castle, the cavemen show up, having followed their tracks, and save the heroes from some Chargin' Chucks with a synchronized tackle.