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.
The countdown of the self-destruct mechanism in Lucrezia Mongfish secret lab stops at seven.
A bit earlier, a salesman in Mechanicsburg shouts about how he haspoiled slurgs for sale. On a stick. One can only wonder if they, too, are steamed in wixxel grease.
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.)
A poster at the Science Fair here: "Planet Earth: A Scary Go Round we live on."
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 fake Jagermeister girls at Mamma Gkika's bar sing a modified version of the Andrews Sisters' song "Too Fat Polka."
Their earlier song is a resetting of "The Beer Barrel Polka" and their show slash song for the "real" Jaegers seems to dance around "You can leave your hat on".
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.)
Bear Doc is suspiciously similar to the main character from The Whiteboard... who's also an anthropomorphic polar bear called Doc. They even have the same glasses.
The Corbettite Order is positively loaded with references to Adeptus Mechanicus
The weapons wielded by the Storm King are a mace named "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.
When Kaja's Author Avatar is being offered drinks on the two-page "Jaegerstomp" spread (during the holiday special arc), all the drinks are from the game Red Dragon Inn.
At first Miss Baumhund looks like Mai Nekota after college. Actually they are both styled after various ladies in the works of Leiji Matsumoto. Foglio drew a couple of issues of the Comico Star Blazers Comic back in the 1980s. The dog/cat name split may or may not be coincidental.
This comic includes a box of Avernum Cigars. Phil has done artwork for several of the Avernum games (notably the pictures for the skills in a couple of the older games are his work, several of which appear as Tropeimages).
When Rivet shows Agatha her collection of tools, Agatha finds a sonic screwdriver.
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!