In the opening credits sequence, when Sheeta falls from the sky (both scene and score piece are quite aptly titled "The Girl Who Fell From the Sky"), the original Japanese synthesizer score simply played normally with only a small difference in composition when the crystal around her neck activated and eased her to the ground, and whatever change there was wasn't even synched to the animation. What was supposed to be an incredible, spine-tingling moment is reduced to simply "huh, that happened". Not so with Joe Hisaishi's reworked orchestral accompaniment for the Disney dub, for when the crystal begins to glow, all music cuts out except for two notes from the trumpets... and then the crystal blossoms into a grand display of blue splendor, the cymbals kick in, the strings and horns blare, and you are simply left with one of the most beautiful moments ever put to film.
That said, many purists excoriated the new score, declaring that it "utterly butchered the film." Perhaps because of the protests, Disney dropped this rescore for the 2010 DVD and subsequent Blu Ray release (but oddly, it is still maintained on the Japanese, UK, and Australian Blu Rays). Ironically, when Disney removed the rescore, fans of the newer score were outraged. (The same is true for the removal of Phil Hartman's extra adlibs for Kiki's Delivery Service.)
The seemingly dormant robot in Tedis Fortress comes alive thanks to a dazed uttering of a spell that Sheeta remembered from her grandmother. Crawling on hands and knees, it blasts the heck out of the entire structure, and keeps on advancing, not even taking a hit from the soldiers' attempts to stop him. Even when the canons on the fortress dents its armor, it still awakens and rips explosions in every direction. Until the Army's battleship Goliath shoots it down with one blast... at which point Sheeta realizes that the robot was trying to save her, not harm her.
The scene where Pazu's entire town leap in on the action and help Pazu and Sheeta get to safety.
The entire scene where Laputa is revealed for the first time, especially how the music swells with each second.
And just before that, Pazu and Sheeta manage to break through Laputa's lightning-ridden hurricane barrier in what amounts to a hang glider, with said scene also subject to a gorgeous Animation Bump leagues above the movie's already extremely high standards.
At the end of the film, Pazu and Sheeta decide to save Laputa by reciting the forbidden Spell of Destruction. The spell literally destroys the black dome containing the superweapons and its manmade walls. Muska falls to his death. At first we are led to believe that Pazu and Sheeta are dead, too, but we later see that they have been protected by the Great Tree of Laputa's roots in return for saving not only it, but the gardens as well.
"Of course! We protected the tree, now it protects us!"
The shirt-ripping scene. Pure, unadulterated, awesome.