Wallace Shawn's portrayal of Manny is very similar to Vizzini from The Princess Bride, who Shawn also plays. He almost uses Vizzini's catch phrase "inconceivable" and has a battle of wits using goblets of "poison" to drink from.
In Chapter 1, when Graham first meets Whisper, Whisper would constantly get his name wrong. Calling him Greg, Grace, Garrett etc. at one point, Whisper calls Graham "Gaston" in which Graham replies "You look more like a Gaston than I do". This is most likely a reference to Disney's Beauty and the Beast. Since Richard White does the voice of both Whisper and Gaston.
The second time Gwendolyn visits with old King Graham, we hear a brief tune play. The song is a gentle version of the Back to the Future theme. Old King Graham is voiced by Christopher Lloyd who played Dr. Emmett (Doc) Brown in the trilogy.
Josh Keaton and Christopher Lloyd provide the voice of young and old Graham, respectively. Coincidentally, Josh Keaton (as Josh Weiner) voiced Jules, the son of Christopher Lloyd's character Emmett L. Brown, in Retour vers le futur (1991) (although Emmett was voiced by Dan Castellaneta in that animated series).
In Gwendolyn's bedroom, you can see a tapestry of the poster from the 1992 game King's Quest VI: Heir Today Gone Tomorrow showing Prince Alexander confronting the Minotaur. Also from the same room, you can see the tapestry of the poster from the 1988 game King's Quest IV: The Perils of Rosella.