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There are references plenty to 80s adventure movies The Goonies and Stand by Me when Tristan, Bakura, and Tea going off to have their own adventure without any main characters. And when they run into Pegasus:
Recently, the episode was edited. Most versions on Youtube will still have the old one from the eighties. Recently, however, the episode was modified to use the theme from Generation 4, which you probably recognize from the sheer presence of its Periphery Demographic.
Kaiba later inputs A-B-A-C-A-B-B, somehow activating "DK Mode" and enlarging Kaiba's head and arms while shrinking his body.note The code actually enables blood in the Genesis version of Mortal Kombat.
Mokuba's 'Ancient Egyptian Cameo' is the opening verse from The Lion King's opening, backwards.
Bonds Beyond Time
Doctor Who - The opening credits, complete with a Duel Monsters card replacing the TARDIS, followed by Yusei's bike making the iconic TARDIS noise when he leaves his era.
After a Master Shake stinger, Mega Ultra Chicken, and the tag team Steves portrayed as the Mooninites, anyone familiar with Aqua Teen Hunger Force can easily see that Little Kuriboh's a fan of the series.
Melvin's obsession with hugs may be a reference to End of Evangelion, where, by the end, all of mankind have exploded into a sea of fuel by the dangerous combination of evil, happiness and hugs. His psychotic nature also hints that he might be aiming for this.
"I'm staring into the distant past. It's sort of like playing Eternal Darkness."
Now expanded in "Meet the Kaiba", with the full first episode with Team Fortress 2 quotes. They work surprisingly well.
Marik Plays Bloodlines has "His hair looks like something out of Space Channel 5!"
Kaiba almost starts singing "Friday". Luckly the camera quickly cuts away.
In a video LittleKuriboh made for a fanartist, Tristan punches Joey and shouts "I am a man!"
Probably an Evangelion reference: In "The Other Abridged Movie," when Gary Stu finds out how long the duel between Yugi and Kaiba will probably last, his internal voiceover frantically chants "I mustn't run away, I mustn't run away, I mustn't run away!"
In the third Lady Gaga parody, we get this exchange: