Episode 2
During the return journey after securing Kaname's notes, the two are chased by a Tokyo Police Mini-Patrol car, which is a spoof of You're Under Arrest. The seiyu of policewoman Youko Wakana is Akiko Hiramatsu, who also played Miyuki Kobayakawa in You're Under Arrest. Kaname also commented on the Skyline GT-R while on the journey returning to the school.
In the preview for this episode, Sousuke says "Next time we use the human-shaped mobile suits called Arm Slaves." This is a reference to the mecha units used in the original Full Metal Panic! series, and more importantly to Mobile Suit Gundam, which pioneered the use of the term mobile suits. In response, Kaname explicitly tells Sousuke that there will be no Arm Slaves in the next episode (or the rest of the series, for that matter).
Episode 3
Student council president Hayashimizu is seen on the beach throughout the episode reading various books. These books are: "The Prince" by Machiavelli, "Death in Venice" by Thomas Mann, "The Elementary Particles" by Michel Houellebecq, "Five Women Who Loved Love" by Ihara Saikaku, and "The One-Straw Revolution" by Masanobu Fukuoka, respectively.
This episode includes a scene reminiscent of a famous one from The Matrix where Neo (Keanu Reeves) seems to dodge bullets in slow motion on the rooftop. This is now known as bullet time. This scene is also has references to Goldfinger, in which Oddjob (Harold Sakata) throws his razor-edged hat as an attack, and Raiders of the Lost Ark, where an expert swordsman gives a display of his aggression and sword prowess by fiercely spinning about his blade. Indiana Jones' (Harrison Ford) reply is the somewhat comedic act of easily dispatching him with his gun instead of his whip.
Just after the bullet time scene occurs, one of the guards says the following line, "Your weapons have no effect on me". Perhaps a coincidence, but this is the same line spoken, several times, from the English dubbed movie Prince of Space.
Episode 5
Three macho brothers have unexpectedly adorable names: Maron (chestnut), Waffle and Chocolat. (For most of the sweets, namely cakes, French words were imported).
Takeshi Aono (the Janitor) is known for doing the voices of typical mad scientists. In the original novel, the janitor's laughter was described as having the same quality of insanity as Jack "Heeere's Johnnie!" Nicolson did in the movie "The Shining." It turns out Mr. Aono did in fact dub his voice in the Japanese TV broadcast of "The Shining."
Episode 6
The author of the "Full Metal Panic!" novel, Shoji Gato, shares the same attraction to women with ponytails as the stalker, Poni-O. However, Gato insists he does not look like the character, including the mask.
Episode 7
The "Training" scene in which Sousuke is training the Rugby Club is reminiscent of scenes from the first half of the movie "Full Metal Jacket" in which the drill sergeant is verbally abusing the troops as part of the training.
Also, the scene when the club is shining and talking to their rugby balls (after their "transformation") is similar to what Private Pyle did in the movie Full Metal Jacket.
If one listens carefully, in both the English and Japanese versions, the voice actors for Sousuke can be heard actually saying the actual vulgarities that are edited out.
Episode 8
The shape of Melida Island where the De Danan is located looks similar to the base used in Science Ninja Team Gatchaman.
"Paladium Reactor" The news of nuclear fusion supposedly created by Paladium electrode in heavy water, as was reported by University of Utah in the late 1990's. However, the experiment could not be replicated, and was thusly disregarded as a hoax. In the alternate universe of FMP!, it has been made usable thanks to advances provided by Black Technology.
Testarossa shower scene in-joke
As Mardukas is threatening Sousuke, there is a short homage to the movie Psycho where Tessa, as she is taking a shower, is attacked by Bonta-kun, armed with a banana. This reference comes from the closing scene of "Ruby Wax Meets... OJ Simpson" that is also a reference to the original source of Monty Python's Flying Circus; Mardukas is British, and in the original novel he makes numerous references to the Flying Circus as Sousuke cleans up his apartment, such as walking behind Sousuke yelling “Hurry up or I'll make you do “Silly Walk” through the base”, and “I'll make you the instructor of self defence against people armed with bananas!” The anime writers removed this scene, no doubt thinking the references to be too obscure; the movie reference was well-known enough on its own, and the banana was left in as an in-joke. The author of the light novels, Shoji Gatou, is a self-proclaimed Monty Python fan.
Episode 9
During the peeping scene after Kazama faints from a nosebleed, he says "She is the best" with his lower face covered in blood, this is a reference to the end of the Full Metal Panic! anime where Tessa says the same thing of Chidori after she gets the sub back under her control.
After Kurz gets shot in the behind by one of the sentry guns during his "peeping mission", there is a parody of Gundam Seed where a "dying" (not really) Kurz angrily urges Shinji Kazama--the only "surviving" member of their group--to complete the mission, despite Shinji's hesitation. Enraged, Shinji charges through the gauntlet of lasers and enters "SEED mode", similar to what happens to Kira Yamato and Athrun Zala--except the image of the seed is replaced by a pair of panties. Everything else is the same--the electric and mental flashes, and the Newtype "pwing!" noise from the original Mobile Suit Gundam series.
Kazama's "I can see the enemies, Kurz!" echoes Asuka's "I can see the enemies, Mother!" in the Evangelion movie, psycho bewildered eyes and all. It can also be replied that in Episode 73 of Saint Seiya, the main protagonist also said the same words before defeating Gemini Saga.
The above could also refer to Escaflowne when Van Fanel becomes able to see the invisible enemies by using the technique Hitomi taught him.
When Kazama jumps into the air and begins spinning around shooting all the targets around him, it appears to be a reference to The Last Starfighter, an 1984 movie about a teenager who is recruited in an interplanetary war after beating an arcade game that is actually a recruiting test. In the final battle, the teenager defeats the entire enemy fleet by using the experimental Death Blossom weapon, which causes the starfighter to spin around rapidly and shoot down all the enemy ships.
The scene when Sousuke is playing ping pong against the wall and the part when Kurz says to Kazama "Run, Kazama, run" are all parodies of the movie Forrest Gump.
Episode 10
"He looks like a dog after all." "You're right" -Kaname & Ren. In fact, the Super Deformed version of Sousuke is usually drawn with dog ears and a tail.
"If I blow the whistle three times, he'll show up." "No Way! That's just like Ambassador Ma(beep)ma!" -Taken from Osamu Tezuka's Ambassador Magma. The beep has to do more with copyright issues than with being obscene.
Yoko Wakina makes another appearance toward the end of the episode. She goes berserk inside a police station by firing P90 submachine guns after she overheard a police officer receive a call about the Bonta-kuns' raid on the Ryujinkai base.
The system boot sequence of Bonta-kun OS is actually that of MSX, the attempt to create standardized computers back in 1983. Microsoft provided the BASIC ROM and various hardware companies (namely Sharp, Casio, and Hitachi--but defintely not NEC, since they already had PC-88 & PC-98 dominating market) built system based on unified standard with enough playroom to give each company their own unique flavor.
Souske's Bonta-kun has an antenna on the helmet, a reference to the command antenna found on the MS-06S Zaku II that Char Aznable pilots in Mobile Suit Gundam.
Episode 12
In the beginning of the episode, Ono D purchased and ate a "Bakunetsu God Curry Bread". This is presumably a reference to the Bakunetsu God Finger, the signature move of the God Gundam, of Mobile Fighter G Gundam fame. It is worth noting that Sosuke and Domon Kasshu, God Gundam's pilot, are voiced by the same actor in Japan (Seki Tomokazu). After the Full Monty bacteria attacks , Mizuki is making Issei the Camel Clutch; a wrestling move originally performed by Ed Farhat better known as "The Sheik". Tsubaki performs one of Seiya's moves when he is about to attack Sousuke but he is interrupted.