Also in the Cinderella parody, the sponsors on the back of the proclamation include "Schlock Mercenary: Cheap Goods for Thrifty Heroes", "Ask Doctor Eldritch: Pets Found! Warts Explained! Crops Blighted! Family Curses Lifted!", "Good food with NO Jagers: Sunset Grill" and "Skin Horse: It's not just for breakfast any more!"
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.
And his first name with the high school that Phil Foglio attended.
If one looks closely, it appears that Doctor McNinja has an office in the hospital at Mechanicsburg. Which... explains a lot. Benjamin Rat appears in that same panel — and "Dr. Rothfuss" obviously goes by Patrick. (The Wise Man's Fear was published three days after that comic.)
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".
It also goes "Spork! Spork" Spork"
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 weapons wielded by the Storm King are a mace named "The Platonic Solid" and a sword called "Archimedes' Lever". But the Jägers call them Smasher and Slasher. This may be a reference to the swords retrieved by Thorin and Gandalf in The Hobbit. They're properly named Orcrist (Goblin-Cleaver) and Glamdring (Foe-Hammer), but the Goblins call them Biter and Beater.
In the comic for Sept 5, 2016 DuPree enthuses about going to Paris because that's where they make those chocolates with the mimmoth note Tiny wooly mammoths centers.
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!