When Kaiba summons XYZ-Dragon Cannon during his fight with Pegasus, the Transformers theme song starts to play.
Yami says "Kaiba, I'm sure on some planet, your strategy is considered powerful, but your weak link is: this is Earth", which was said in Kung Pow! Enter the Fist.
When looking for Yami in the labyrinth, Yugi shouts "KHAAANNNNN!" in frustration.
After Bakura reveals a segment of "Zorc And Pals" and asks what Yami thinks of it, Yami says "I think you'll be taken off the air faster than you can say Arrested Development"!
Right before Yugi mind-crushes evil Bakura, Yami says "Finish him!"
This episode also contains the, "What is a man?" dialogue.
In the same episode, Yami starts listing spoilers because the villain is an obvious fan of plot twists. He's cut off by a title card, but 3 are heard that sound oddly familiar...
"Impact with ocean imminent. I hope you all played BioShock."
"All your questions will be answered in due time. In the meantime, prepare to be assimilated! Resistance is futile! [Cue crapload of other movie references.]"
After entering a room with four doors with symbols above them, Yami states "Oh lovely. A rejected puzzle from a Professor Layton game. That's just fan-tucking-fastic."
The maximum level on the Jiggle-o-meter is labeled 'Faye Valentine'.
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.
Paradox having Mandark's laugh is also reference to the Dexter's Laboratory movie which has a similar plot ("I am here for the one who destwoyed the future!").
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."
In the 2010 April Fools video, the opening for the fake 5Ds Abridged Series is an homage to the show's opening, complete with the camera zooming in on Jack's mouth before the theme kicks in.
In recent episodes, he and Linkara have mutually referenced each other, culminating in each doing a cameo line in the other's video.
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!"