Alice in Wonderland Jr. uses the first line of music from "It's A Small World" when Alice shrinks.
The introduction to the Caucus Race has a few measures of "Under the Sea".
Wicked has a metric ton of these, mostly based on the the original Wizard of Oz film. Best example is probably
What's in the punch.
Lemons and melons and pears.
The 1995 concert version of Anyone Can Whistle had Angela Lansbury as narrator stating that she was the mayoress of a town much like the one in the musical some 31 years ago "for a very short term." The original production opened in 1964, and ran on Broadway for only one week.
In the 2011 Broadway revival of Godspell, "Save the People" ends with Jesus picking clothes out of a costume-rack, including the Superman-styled t-shirt (a reference to his costume in the film), which he rejects.
In The Golden Apple, one song has the refrain, "Circe turns men into swine." What makes this a Mythology Gag is that here it's only a metaphor.
In Pokémon Live!, as in the Pokémon anime, Jigglypuff scribbles drawings on Ash and co. when they fall asleep after she sings.
A Dodrio can be heard giving a morning crow like one does in episode one of the anime.
Charlie's "How'ja do?" Catchphrase in Act One is inspired by the Breaking the Fourth Wall introduction to the character in the opening chapter, in which he, via the third-person narrator, greets the reader with "How d'you do? And how d'you do? And how d'you do again?"
Mike Teavee's favorite videogame is Captain Knuckleduster, a title inspired by the novel's counterpart loving TV shows with gangsters "giving each other the one-two-three with their knuckle-dusters!"
In the novel, there many inventions of Mr. Wonka's that are only discussed or mentioned in passing such as ice cream that never melts, Eatable Marshmallow Pillows, and Fizzy Lifting Drinks. Those three and several others are worked into this adaptation...as ideas Charlie has. (This is significant.)