- The entire series is an homage to Mars Attacks!, Men in Black, Invader Zim, and other alien related movies and shows.
- The Blue Moon Drive-In Theater during Teenage Zombies From Outer Space before changing the film is playing a clip from the infamous movie Plan 9 from Outer Space. You get to see some b-movies from the 1950s (most of which being the more So Bad, It's Good ones) in the Archives of the mothership.
- Crypto and Pox both discuss possible future Video Games in the third game, giving shout outs to Super Mario Bros., Sonic the Hedgehog, Halo, and games based on movies, all in the same conversation.
- Path of the Furon has the mission Close Encounters of the Furon Kind where you have to reply to cultists beeping tones at your ship.Pox:Great Arkvoodle! The fools think we have a musical language!Crypto:Nobody talks music, that's stupid!Crypto: (To Dr. Go!) My name is Luk-I mean, Cryptosporidium. I'm here to rescue you.Pox: (In reference to Crypto being Son of Arkvoodle) Crypto! What if it's true?! What if you're THE ONE?!
Crypto: Well, I did take a red pill this morning, heheh.
- Seen when reading the thoughts of a female hippie resident of Bay City:'' "The Adventures of Luke Starkiller? Ha! Dream on, Georgie boy!
- Panicking citizens of Albion may spout references to Quatermass, David Bowie, and Doctor Who. Throw one with your saucer's tractor beam or Psychokinesis and one citizen may just scream, "Double-plus ungood!", which is also heard sometimes when the alert level in Albion goes to tred.
- Some of the armed Cosmonauts in the second game might tell Crypto whilst attacking "In Space, no one can be hearing you screaming!"
- "Mighty Morphing Power Alien!"
- The Fantasy Atoll level in Big Willy Unleashed is a giant shout-out to Fantasy Island, right down to expies of Mr. Roarke and Tattoo (only with the bodies flipped).
- In the first game, Crypto is a red-eyed, genitalia-lacking space alien.
- Silhouette, female badass extraordinaire, known only by her code name, is a patriot.
- In the fourth mission of Takoshima, if you try to talk to Professor Yuki with a non-White Ninja disguise, Crypto will attempt to hit on her, only for it to fail:
- This is also parodied in the thoughts of a Japanese co-ed, who claims she'll kick a GI agent in the nads if they say this to her again.
- Some of the Free Love quotes pedestrians say make reference to songs that are popular during the 60s. Some examples are Sex Machine, Creeque Alley, and many by The Kinks and The Who.
- A passing reference to Steely Dan is made during the cutscene in "Where Have All The Flower Children Gone?", when Coyote Bongwater is finishing his meditation session with two female hippies.Bongwater: Remember, wherever you go, I'll be there. The shine of your Japan, the sparkle in your China.Female Hippies: Bodhisattva, Bodhisattva.
- Also serving as a Take That!, while reading the minds of the inhabitants of Takoshima, a kamikaze soldier will have this thought:"Hey Mickey Rooney, I saw Breakfast at Tiffany's, and I know where you live!"
- Sometimes, while using Psychokinesis on multiple objects in Bay City without destroying or killing anyone, a female hippie will say "What's the buzz? Tell me, what's a-happening! followed by a quick giggle. Crypto also says this quote before starting "From Russia With Guns".
- When Armquist shows up in a Humongous Mecha after Crypto agrees to "do things [Armquist's] way":
- The opening scene of the second game features this when the KGB assassin approaches Crypto.Crypto: You expect me to beg, human?KGB agent: (points gun at Crypto's face) No, little Furon, I expect you to die.
- There are several towards The Graduate in Bay City during the second game:
- The Gene Blend that makes body-snatching easier for Bay City women who are squares is titled "Hey Mrs. Robinson!".
- In another reference to The Graduate, a Bay City hippie might think about "plastics".
- "Wanna hear the sounds of silence?"
- Scare a Bay City hippie, and he might go screaming for Elaine.
- Patty Wurst in Big Willy Unleashed addresses that Big Willy's is people.
- In Bay City, you can find posters advertising Captain Beefword.
- Among the lines that Pox can say if you try to buy an upgrade without enough DNA:
- Pox delivers a Precision F-Strike Shout-out when he's unsuccessful in phoning home for backup after the mothership is destroyed.Admiral Cyclosporiasis: This conversation is over. Sit tight, I'll send someone to pick you up as soon as I can spare a rescue pod from the fleet. [hangs up]
Pox: Hello? Hello??? Frak!
Pox: Ancient Cylon curse word.
- A hippie leader in the second game can be heard yelling "This is the spawning of the cage and aquarium!", a nod to the They Might Be Giants song "Cage & Aquarium", which was a riff on "Aquarius" from Hair.
Shout Out / Destroy All Humans!