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Top Gun
Stewie refers to Brian as "Goose", which is a allusion to the movie Top Gun.
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Jerky Boys
During the scene where Mort is talking about what the Nazis would do to him if he were captured, he uses phrasing from his Jerky Boys prank phone call CDs featuring the character Sol Rosenberg.
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Coca-Cola Commercial
"Mean" Joe Green: Hey kid, catch.
(Tosses the uranium to Stewie)
Stewie: Thanks "Mean" Joe!
This is alluding to the Coca-Cola commercial where a kid gives Joe Green a coke and in return "Mean" Joe gives the kid his jersey. The commercial aired in 1979 during the Super Bowl. This joke was previously used in the episode 'Peter, Peter, Caviar Eater' except it was Peter in that episode instead of Stewie.
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Indiana Jones
When Mort, Stewie and Brian escape the crashing plane on an inflatable raft, they're referencing Indiana Jones and The Temple of Doom, while the chase scene featuring the Nazis on motor bikes resembles Indiana Jones and The Last Crusade.
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Disneyland
The motto displayed outside of wartime Berlin -- "The Happiest Place On Earth" -- is also the motto of this theme park.
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German Scientist: We're having much better luck developing this impressive collection of 100 Luftballons. (One of the balloons bursts).
A reference to a song called 99 Luftballons by Nena from 1983.
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German UBoat Soldier: Ach! unsere Unter See Bootsen schtielen mit ein dog und baby und Art Garfunkel.
Mort Goldman is mistaken for Art Garfunkel who is an American singer/songwriter (born 2 years after this episode is set). He was, however, of Romanian Jewish descent.
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Star Wars
When Stewie, Brian and Mort steal the German officers uniforms, you can hear a spacelike gunshot. This gunshot is similar to Star Wars when they shoot the Stormtroopers for their uniforms.
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Little Shop Of Horrors
Rick Moranis' explanation of how he saw Mort step into the time machine with the aid of the back-up dancers was set to the tune of Da-Doo from the classic musical.
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Back To The Future
This episode had a lot of references to Back to the Future. The way Stewie and Brian enter 1939 is similar to the way the DeLorean appears. During the scene where Brian, Stewie, and Mort are being chased by Nazis, the music playing during the scene where Marty is being chased during Biff and his gang. Also, Stewie uses a custom-made skateboard to escape the Nazis and leaves them to crash into a manure truck, just as Marty did.
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Duck Soup
The mirroring scene between Stewie and Hitler is a reference to this Marx Brothers film.
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Flash Gordon
The scene of the winged soldiers attacking the German planes is a reference to this film.
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Blues Brothers
After the German piloted U-Boat crashes on the sea floor a number of police cars pile up alongside it. This is a reference to The Blues Brothers, where several times while chasing Jake and Elwood the police end up in large pileups.