The scene where Luigi and Mario getting out of the cave. Immediately after Luigi squeezes out of the hole he dug, he runs back in the cave, which is sealed by a wooden gate, and tries to hide from the Hammer Bro. By running through the gate and breaking it.
Die for Our Ship: Going by YouTube comments, Prince Haru comes under fire a lot. Anger and sadness can do that to otherwise stable fangirls and fanboys.
Ear Worm: That song that plays over the opening credits.
Hilarious in Hindsight: In Mario's fight with Bowser, at one point, he grabs Bowser by the tail and throws him away. Guess what you have to do in Bowser's boss battles in Super Mario 64. Additionally, one scene in the film also involves Mario entering a sunken ship, just like in 64.
This film used the idea that Bowser is in love with Peach years before Paper Mario 64 practically made it canon.
Luigi in this film wears yellow and is obsessed with money, just like the later character Wario.
It's not as egregious as Bowser, but Peach is voiced by then-popular J-pop singer Mami Yamase. The fact that she's an idol and not an actress is apparent, and not helping is that she makes the seemingly adult princess sound like a petulant, nasally ten year old.