Unreliable Narrator: Klaus encoded a message to his son in a story he tricked Phil into delivering. Although we only see the tail end of Phil's version, it's clearly different, and judging by Gil's reaction he screwed up most of the symbolism (that is, the entirety of the message) too. Luckily, Tarvek notices something is up.
Subtle, but when the Jägers are clapping, the sound effect is in the Jägers' accent. This one comes up a handful of times throughout the series. Just about every time a sound effect shows up for one of the Jägers it's in their accent.
Up to Eleven: The "Movit" series of stimulants comes in a verity of intensities, the strongest of which appears to be 11. Previously, it was thought that the strongest was 6, which itself is one above the common 1-5 scale. As one might imagine, the further up the scale, the more one blurs the line between "powerful stimulant" and "lethal injection."
That section of the story is even called "Zola Goes up to Eleven".
Vetinari Job Security: Hilariously deconstructed with Baron Wulfenbach. He completely fits the description in that he is so important and necessary for the continued functioning of Europa that only a madman would think about overthrowing him. Unfortunately, this being Girl Genius, there are powerful madmen (a.k.a. Sparks) everywhere, which is why there is nearly always a rebellion somewhere. Further illustrated in that, as soon as he is hospitalized (and possibly killed), the whole continent immediately erupts in chaos.
Weasel Mascot: The Wulfenbach Bug Squad (aka the Vespiary Squad) of course! Apart from their uniform's Nice Hat of a slaver-wasp skull, this is their main hat. Their charges are all modified weasels, without which the Squad could not do their job as wasp detectors and exterminators. Although they have eight legs, they are still, very much, weasels of some description (however big they get). And, they are sooo cute (for a given definition of cute).
What Happened to the Mouse?: The monster horse that appeared during Master Payne's Circus story: we never know why it was/turned into such a hideous abomination, and it was never addressed again. Likely just because a spark felt like it, and because monsters are so common in this setting that it is a mundane hazard.
A little earlier we have Zulenna, she gives her life to save Agatha and the others, gets put in a healing chamber and seems to set up a plot point about Klaus getting grief from the Fifty Families about resurrecting one of their number.
The Baron cloned Olga's body, assuming her to be the believed-dead Agatha. Nothing on what happened to the new body.
What the Hell, Hero?: "TRULY YOU ARE YOUR MOTHER'S CHILD!" More understandable than some, since the one calling Agatha out murdered her parental figures in cold blood, but everyone Von Pinn worked with considers her tough but fair, and likes her. And she is the closest thing Gil had to a mother. Agatha's response is a heck of a lot of guilt.
The Sparks, by definition; Baron Wulfenbach fights this off by pure force of will... usually. Every successful Spark has at least one very level-headed keeper.
The Heterodyne family in particular. Apparently their unearthly strength and stamina comes from drinking from a spring famed for causing insanity and death in people who just bathed in it.
It's implied that the reason the Storm King was regarded as the greatest king of all time is because he was able to keep enough self-control to rule effectively. This may have been at least partially due to the influence of the Muses.
World of Badass: Show us a character who's notBadass, and within a couple of strips they'll either turn out to be badass or they'll be dead. In a world ruled by mad scientists, even the minions and staff have to be pretty tough to avoid getting killed.
World of Buxom: Just about every post-puberty female character, notably Agatha, Zeetha, the Geisterdamen and Mama Gkika. The Muses and Clank Anevka have pretty darned voluptuous figures, too. The only exceptions are Rivet, Wrench Wench for Master Payne's Circus; Daiyu, the doctor's daughter (who would be decent-sized in any other work); Grantz, the immensely strong monster hunter (who falls firmly into the Bifauxnen slot); and Miss Baumhund, the lanky grad student (who has only appeared in that one strip — so far), who seems a bit out of place when compared to other female characters.
This is Agatha's attitude in the Cinderella play to being grounded. Of course, she was grounded after tricking Mamma Gkika's "Evil Stepmother" into putting her fist through a hive of specially-bred quilting bees.
And in a more serious tone, Klaus's attitude to the pain he suffered getting to the window and back. Not only that, Klaus actually said that if the experience paralyzed him for the rest of his life, it would still be worth it after seeing his son pull off that moment of awesome.
Would Hit a Girl: Pretty much everyone, since there are more than enough dangerous females to dispatch anyone reluctant to fight back. Some notable examples:
Ardsley Wooster punching Bangladesh DuPree in the face.
Airman Higgs beating the crap out of Zola.
Tarvek absolutely losing it when Zola tries to kill Agatha again and brutally beating her — and then trying to strangle her to death.
There's one counting the days since the last hideous death. Considering the Castle's nature, this may be a way of keeping score. (Although, the sign might not be accurate any more, since the guy whose job it was to update it died a hideous death.)
Zeppelins from Another World: Lots. Predominantly used by the Baron; he has his entire command center in Castle Wulfenbach, a zeppelin of truly Brobdingnagian size, equipped with numerous labs, docking bays for several smaller craft, and penthouse-like living quarters on top of the hull. It coms with an entire support fleet, and several other of the Baron's troop units are zeppelin-based. Which is of course very practical if someone makes the Baron "come over there".