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.
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.
One scene in the film also involves Mario entering a sunken ship, just like in SM64.
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.
They Just Didn't Care: Upon obtaining the fire-flowers, the Mario Bros. use them to defeat a pair of Buzzy Beetles, the one enemy that is immune to fireballs.