The show's Art Deco aesthetics and spray-painted backgrounds drip with homage to Metropolis, especially its posters.
Why does Vladimir/Mr. Scruffles and his fellow lab rats want revenge of Mrs. Wakeman? Because she altered their bodies to resemble Mickey Mouse. And at the end of their debut, Wakeman holds up a familiar pair of pants for Vladimir to wear...
That episode was also an allegory of the Soviet revolution; the leader's name is Vladimir, he speaks in a Russian accent, calls his fellow rats his "comrades", there's a Russian-style music score throughout the episode, and there's even a hammer and sickle in the episode's title card.
In "Around the World in 80 Pieces", there's a giant kaiju monster attacking a Japanese city. The monster has the same roar as Godzilla.
The male half of the alien couple in "Unlicensed Flying Object" sneaks one in.
Alien: Yeah, well, personally I can't wait to get off this hick planet! Bunch of rip-off artists, these earthlings: five bucks for a cup of coffee, no Extraterrestrial discount at the hotel, and I know that bellboy stole my tricorder.
Lancer - upon seeing Jenny's ridiculously big ears - quotes Dumbo.
Lancer: I've seen a peanut stand; I've heard a rubber band; I've even seen a needle wink its eye...but I think I've seen about everything when I see an elephant-eared robot girl!
Lancer's design is inspired by the symbol◊ of Walter Lantz Studios, which depicts Woody Woodpecker dressed as a knight on a horse, as seen in the opening of many of their cartoons.
In "Future Shock" when Jenny gets to the Vault: Jonny Quest, Batman, Tintin and probably a couple others.
The Cluster (for the most part a fully roboticised version of the Borg from Star Trek) uses the "resistance is futile" line.
Vexus says "be seeing you" to Jenny in her first appearance, complete with the same hand gesture.
In the same episode, the fading to Jenny's original self when she's cured parallels Lawrence's death and transformation back in The Wolf Man (1941).
The bad guys in the first part of "Speak No Evil" are a reference to Zedd's Z-Putties in Mighty Morphin' Power Rangers, in that they're both easily defeatable via obvious targets somewhere on their bodies.
"Escape From Cluster Prime" references the cat bus from My Neighbor Totoro.
In "The Puppet Bride", the boy that eventually finds Little Acorn looks identical to Lucas from Mother 3.
That episode is also based on the original story of Frankenstein.
In one episode, Tuck calls Dr. Wakeman to get Jenny and Brad in trouble for throwing a party while she is away. When Brad decides to let him stay for the party, Tuck responds to Dr. Wakeman's "Hello?" with, "I just called to say I love you."
When Jenny's identity is outed on Cluster Prime, a robot points at her, drops its jaw, and starts shrieking in a similar manner to Donald Sutherland in Invasion of the Body Snatchers.
Sheldon and Nora argue and eventually brawl over their techniques in getting to Cluster Prime, causing each of their machines to topple into each other, resulting in an exchange worthy of a Reese's Peanut Butter Cup commercial.
Nora:Hey! You got your time fissure capsule in my quantum defibulator!
Sheldon: You got your quantum defibulator in my time fissure capsule!
[The machines activate and open a portal to Cluster Prime]
Sheldon: Two great machines...
Nora: ...that work great together!
After Brad finds out that Melody is a robot, he asks how he can trust her again, and she kisses him. His response: "So she's mechanical!"
One to John Carpenter's The Thing (1982) of all ...things, in "Toying with Jenny." After Tuck tears the head off of one of the dolls, it produces four spider-like legs from its neck and walks away.
Also in "Toying with Jenny," the scene of Tuck's Jenny figure crawling out of the trash and coming to life prematurely, leading Tuck to find it under one of the sofas and realize that it does not have any batteries installed as its Exorcist Head abruptly spins around 180 degrees to look at him, is an homage to Chucky in both Child's Play (1988) and Child's Play 3.
In "Stage Fright," Jenny and the other Tremorton High students being mesmerized by the deceptively beautiful appearance of the flame aliens that then proceed to attack them, and Jenny only being able to defeat them by not looking at them, references The Ark of the Covenant scene from Raiders of the Lost Ark.
In the beginning of "Killgore", the toy store manager calls him Kilroy.
Sheldon's training sequence in "Agent Double-O Sheldon" spoofs J's in Men In Black.
When Jenny passes through a convention in "Infectious Personality", one of the con-goers wears a cardboard box over his head with a downward-facing arrow on the front, which looks a lot like an airbending tatoo.
In the pilot Jenny eats an ice cream cone, only to open her stomach and take it out, much like Astro Boy.
After a robot takes control of Tuck's body he forces Brad to build him a snow fort after telling him "You are not the boss of me now"
In "Weapons of Mass Distraction", Travis' father is actually The Tramp from Modern Times
In one episode, after Jenny is powered on, she says "Happy Birthday!" à la Frosty the Snowman.
One of the episodes from the first season was titled "Daydream Believer". Additionally, when Jenny ends up getting stuck in a nightmare mid-way through the episode, her surroundings look very Dr. Seuss-esque.
◊ of Walter Lantz Studios, which depicts Woody Woodpecker dressed as a knight on a horse, as seen in the opening of many of their cartoons.