When Zola first shows up claiming to be the new Heterodyne daughter, Agatha complains about her being a terrible, cheesy actor. Zola's very next line? "Yonder lies the castle of my father!", a quote from The Black Shield of Farnsworth, which is generally considered one of the worst-delivered lines ever as the original actor had a very strong Bronx accent. usually rendered as "Yonda lies da castle of my fadda" to emphasise that Curtis was Not Even Bothering with the Accent.
The nefarious Prince Aaronev Wilhelm Sturmvoraus is visually based on Phil Foglio's fellow webcomic artist and Dragon Magazine alum Aaron Williams, and his servant Nodis Williams's signature character, Nodwick. Also, Aaronev's dogsbody Artacz, who looks like a younger version of Artax from Nodwick, only with a shorter moustache.
The Cinderella parody features music by the P.D.Q. Bach Engine, whose operator bears an uncanny resemblance to Peter Schickele.
Gil's Runcible Gun, which shoots sporks, references the "runcible spoon" mentioned in "The Owl and the Pussycat".
The introduction of Those Three Jagers has them hanging from a gallows for days, which is likely a shout out to the late Robert Asprin's Myth Adventures series (Phil Foglio illustrated the comic version.)
The beginning of Chapter 6 in Agatha H. And The Clockwork Princess to a certain infamous play ......
Lucrezia: You sir, should remove your pants. Stranger: Indeed? Judy: Indeed, it's time. We have all laid aside modesty but you. Stranger: I... wear no pants. Lucrezia: (Terrified, aside to Judy.) No pants? No pants!