To get the most obvious out of the way, the style of the art, tone, and episode structure resembles The Powerpuff Girls.
A pair of beautiful angels who wreck havoc wherever they go? One of which has bright, messy hair with a harsh attitude and the other long, darker hair with a (slightly) more controlled personality? They could almost be stand-ins for the girls from Dirty Pair Flash.
The Demon Sisters, despite having horns and bright-red skin, often remain disguised until they reveal themselves by throwing off their costumes in one swoop - which directly mimics Team Rocket's antics in nearly every episode of Pokémon.
Panty & Stocking with Garterbelt: The Original Soundtrack
The episode could be a reference to the Powerpuff Girls episode "Town and Out" (which had the girls moving to a much more realistic city).
Also, the Art Shift has been compared to the styles of both Satoshi Kon and Studio 4C. In reality, the episode was referencing something much more obscure - Shinya Ohira's episode of The Hakkenden, which angered many fans as a result of its realistic, "ugly" aesthetics and loose style. This reaction mirrored the one that fans had while watching Osamu Kobayashi's episode of Gurren Lagann, episode 4, and this episode could easily be seen as an attempt to create a similar reaction.
The beginning of the episode features a Buddha-like Omi doll.
The ghost that the Optimus and Megatron homages form into looks like the Fallen.
Unicron pops up at the end of the episode.
Panty and Stocking's transformed versions are each a mix of the original cartoon's and the original movie's faction leaders: Panty is a mix of Optimus Prime and Rodimus Prime, while Stocking is a mix of Megatron and Galvatron (with Animated Megatron's swords).
For what it's worth, the Japanese voice cast outdoes the dub in that regard; the voices for not-Optimus and not-Megatron are actually the same voice actors as from the Japanese dub of the G1 Transformers cartoon.
Also the Starscream expy sounds kind of like its G1 self
And there's also iconic lines from the G1 movie like "one shall rise, one shall fall" and "why waste your life".
The title is a reference to George Romero's "Dead" series. This title could also be referencing the anime/manga Highschool of the Dead, the chapters/episodes of which are often titled as a main theme of the episode, plus "... of the Dead".
The way Garterbelt uses his Shotgun is the same manner as the reverend from From Dusk Till Dawn. Also the dildo contraption Panty uses as a weapon is a direct reference to a similar weapon used by George Clooneys character in the same movie.
Part 1 as a whole feels like a homage to Tom and Jerry and similar old style cartoons.
In Part 2, after being microwaved, Chuck reforms itself pretty much like Watchmen's Dr Manhattan after being de-atomized.
The scene where Chuck punches a fly on the wall and gets hit with a constant stream of flies is a parody of a scene from Evil Dead 2, where Ash gets sprayed in the face with a stream of blood coming from a hole in the wall.
and finally, King Crimson's In The Court Of The Crimson King with Garterbelt's screaming face
When PSG is playing beneath the Northern Lights background, Chuck is wearing Kenny's parka. Moreover when they are playing at Times Square, a billboard for UFC could be seen as well as the storefront for the now-defunct Virgin (or, rather, Virginia) Megastore.
Panty's plan to have sex with 1000 men before returning to heaven exceeds the goal of another anime heroine by exactly one order of magnitude.
The scene where Panty and Brief look at each other through an aquarium is an homage to Romeo + Juliet. It even features a Suspiciously Similar Song of the song used in the equivalent Romeo + Juliet scene.
The group of men Panty has sex with in the beginning look an awful lot◊ like Gary Oak.
In that very same image, the Ghosts pursuing Brief look like a bunch of demonic Totoro!
Panty's hairstyle at the party lends her a rather astonishing resemblance to Winry Rockbell.
Her entire outfit is actually a homage to an outfit Taiga wears in Toradora!
The angel wings she has on also makes her more like Juliet in Romeo + Juliet.
Brief says "I'm not your doll anymore" to his father. Rei Ayanami says that to her "father" Gendo Ikari in episode 26 of Neon Genesis Evangelion.
The "ALART" that appears on Garterbelt's scanner thing is most likely a shout-out to Neon Genesis Evangelion, and not just a typo like most people assume it to be. It's changed back to "ALERT" in episode 13.
Corset's plan is to arrange a marriage between Brief and Scanty, then use Brief's penis atop a symbolically-shaped tower as the key to release an Eldritch Abomination. Sounds awful familiar, and considering the Ghostbusters shout-out with Brief mentioned above, probably not coincidental.