- Mardukas is a Monty Python fan, as mentioned in the Cool and Unusual Punishment entry; since they couldn't use these references in the anime, they settle for a more subtle Shout-Out when, in a parody of the Psycho shower scene, the attacker wields a banana.
- In the English dub, whole quotes from a certain Drill Sergeant Nasty from Full Metal Jacket are used for the Rugby team's Training from Hell. Even without that, near the end of their training, the Rugby team members started talking extremely... affectionately to Rugby balls that they were cleaning.
- In a later episode in which Shinji goes into SEED mode.
- In the first episode, the teacher searches Kaname's schoolbag and sees a copy of So Long, and Thanks for All the Fish.
- The OAV that comes after The Second Raid features an Affectionate Parody mashup of Future Boy Conan and Detective Conan called Future Detective Boy Conan, depicting a famous scene from Future Boy Conan with the addition of glasses and a bow tie. The video box cover is also seen, and is a parody of the cover of Future Boy ConanJimsy from Future Boy Conan is given the face of Detective Conan's Mouri Kogoro.
- Two major shout-outs to Neon Genesis Evangelion in Always Stand By Me (Part 2): Sophia/Chidori wearing a Rei-style plugsuit, and Al stopping an incoming nuke with an AT Field.
- Captain Sailor of the U.S.S Pasadena is shown shaking three ball bearings. And one of his superior officers refers to him as Ahab.
- The Pacific Chrysalis events has several shout-outs to Die Hard.
- And the submarine battle during those same Pacific Chrysalis events are very reminiscent of The Hunt for Red October, including Mardukas being a British version of Marko Ramius.
- One of the Yakuza in episode 10 mentions Osamu Tezuka's manga, Ambassador Magma, when Kaname says she summons Bonta-kun by blowing her whistle three times. The picture of Magma's spaceship and yakuza's voice were censored due to "copyright reasons."
- In episode 6, Kaname compares Sousuke and Kurz to Butch Cassidy and the Sundance Kid, and their situation to the Trope Namer for Bolivian Army Ending.
- Reading the novels, it becomes apparent that Gatoh is a Tom Clancy fan: Kalinin's wife dies in the same manner as Marko Ramius' wife, prompting his defection; the three USN submarines that appear in FMP also made appearances in Clancy's books.
- Bonta-kun is an obvious Shout-Out to Gonta-kun, the mascot of the classic children's educational show Dekirukana.
- The Filler episode "Is Narashino Burning?" (episode 14 of the first anime) has a lot of Gundam references. The head of the Nerima Red Dragons is a nod to Char Aznable. He loves the color red, has swept-back blond hair and sunglasses, flirts with younger women, and (at the end of the episode) starts to deliver Char's famous "mistakes of youth" speech. Chidori lampshades all this by asking "Is that supposed to be cosplay?" when she first meets him. When Sousuke shows up in an AS, we're told it's moving three times faster than a normal AS, which was supposedly an attribute of Char's Ace Custom Zaku II. Finally, the Red Dragons's Red Stream Attack is a reference to the Jet Stream Attack used by the Black Tri-Stars in Mobile Suit Gundam, complete with three machines charging an enemy in a straight line and one jumping over its partners (as well as the hero using one of the enemy machines as a springboard, as Amuro did against the Tri-Stars).
- Furthermore, the box for the Arm Slave model kit in this episode resembles a combination of the boxes for Bandai's EX Modelnote and High Grade Universal Centurynote lines. It's even said to be made by Banpresto, a division of Bandai (though one that usually makes video games like Super Robot Wars).
- In an episode of The Second Raid, Kaname is watching a TV show that appears to be Spider-Man IN FEUDAL JAPAN!
- Upon discovering that Mithril will not be able to install him into another AS, Al requests to instead be installed into a car - preferably a Trans Am.
- From the anime soundtracks, the tune "Tokkou Yarou" is an homage to the the theme from The A-Team, while "Shissou" from The Second Raid homages the theme from Airwolf.
- The episode name "Welcome to the Jungle".
- In episode 5 of Invisible Victory, one of the Arm Slaves in the Giant Killing match has the same paint job as a Dom from Mobile Suit Gundam.
Shout Out / Full Metal Panic!