Big Bertha's Establishing Character Moment features her casually tossing the old woman trying to rob Mario and Luigi off a bridge, taking the meteorite piece and daring Mario and Luigi to get it back, and using her stompers to jump across the entire square before walking off.
Mario takes her up on the challenge and essentially seduces her in a gambit to steal the meteorite back. It's so audacious and well executed that she isn't even mad afterwards.
The Devo Chamber scene. After Koopa demonstrates the De-evolution process by turning Toad into a Goomba, Mario shoves the tyrant into the Devo chair. The Brothers beat up the guards and give Koopa a taste of his own medicine before escaping. While the de-evolution doesn't take effect, Koopa's fury at what the brothers did is palpable. "I'll kill that plumber!"
Mario: You're going back where you belong, lizard!
Faced with climbing Koopa's gargantuan tower, Mario and Luigi turn off the heating system to buy time to rescue Daisy, since reptiles are cold-blooded and it would slow them down.
Yoshi utilizes one of his game abilities with his long tongue, tripping and biting Lena and allowing Daisy to escape.
When Toad the Goomba is set on fire, Daisy uses a fire extinguisher to put him out, initiating his Heel–Face Turn.
At the Boom Boom Bar, Lena successfully steals the meteorite back from Mario and Luigi, ensuring her scheme of world domination comes very close to succeeding.
The elevator scene. Starting with the brothers donning their coveralls and ending with Luigi making the Goombas dance to stop them from noticing them.
The mattress chase scene has Mario and the Brooklyn girls ride down a giant frozen pipe and use icicles and Mario's tools to trip up their pursuers. It's really enhanced with the music.
The Thwomp Stompers are jet boots that emulate the jump height from the video games. Big Bertha shows them off in the beginning of the movie, and Mario and Luigi later weaponize them against Koopa and his army.
Mario bluffing Koopa by pretending his shoelace is the meteorite necklace to buy time for Luigi to get to the real rock.
The Bob-Omb. To quote Destructoid's list of why the Mario movie is underappreciated:
Mario stands on a bridge, weaponless and defenseless. King Koopa stands across from him, armed with a flamethrower. What does Mario do? He takes out the small windup bomb given to him by the old, fungi-fied king and proceeds to wind it. Koopa squints, trying to see what he's doing. Suddenly, the realization hits him: "Bob-omb." At this point, everyone in the city sees what Mario has in his hands, and they proceed to FREAK THE FUCK OUT. Cars crash, people trample each other in an effort to run away, and chaos generally ensues. All based around a small black ball wearing plastic Reebok shoes (seriously, the Reebok logo is on the Bob-omb's shoes. I'm not posting a capture of it, you'll have to look for yourself). There isn't a kid alive who saw the movie and didn't want one of these.
Then later, the bomb detonates, creating a decent explosion that launches Koopa several dozen feet into the air. Yeah, it may be cute and adorable, but a Bob-omb is still a bomb, and bombs explode. The thing is basically a wind-up hand grenade. No wonder everyone panicked.
The special effects. This film had to literally invent new technology to make much of its visual effects look as realistic as they do. Unfortunately, Jurassic Park's effects were a much more explicit focus, so it gets more attention for its influence on the industry.
Daisy's face appears out of a formerly solid rock wall like it's engulfed in sand.
Yoshi. For an animatronic puppet, it looks like it just stepped out of a time portal to the Jurassic Era. He looked so good, in fact, that the creators of Jurassic Park actually studied his puppet to get off the ground with their T-Rex.
This also applies to the Goombas. All of them, including those only seen in the background, had multiple movements built into the heads.
The pan over the city towards Koopa's tower. This was done by one man over a period of six months and was deemed impossible beforehand.
The CGI Tyrannosaur looks amazing as its form morphs and solidifies before turning into slime, especially for the time.
The King turning back into a human from his fungal form is done near-seamlessly and without cuts.
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