* John Lennon vs. the Dreadful Flying Glove.
* And just before that, the Beatles beginning their counter-attack against the Blue Meanies by playing "Sgt. Pepper's Lonely Hearts Club Band".
* When the Beatles team up with their Pepperland counterparts, the real Paul shouts, "Beatles to battle! CHARGE!!" And Ringo tops it off with an appropriate fanfare from a trumpet, even when it's quickly cut off by an incoming blue arrow.
* The camera floats up through the roof of Pepperland as The Old Mayor is apple-bonked to death and Fred escapes JustInTime to the opening strains of the title song.
* "First time I saw that 'Nowhere Man', that Nobody... ''I'' knew he was Somebody!"
* Music/TheBeatles [[spoiler:finally putting in an appearance at the end]].
** Furthermore, how the filmmakers managed to change the Beatles' minds about the film. It was made out of contractual obligation, so the band wasn't all too keen on the idea initially (which is why their voices were provided by different actors), but after seeing previews of the film they changed their minds instantly. It was too late to voice their own characters, but they gave the filmmakers a few unreleased songs [[spoiler:as well as their cameo in the very end]].