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I really liked the part just after Yusei, Jaden, and the Crimson Dragon arrived in Yugi's time. The look on Yugi's face as they drop him off after rescuing him was priceless. Not to mention that holler!
Little Yugi: WHOAAAAAAOH!
Bonus for Jaden and Yugi's expressions on the D-Wheel compared to Yusei's regular calm look on his face
The chattiness of Dark Magician and Dark Magician Girl, particularly compared to Junk Gardna, who's a robot, and Neos, who's mute. Given what they're facing, it borders on Casual Danger Dialogue at times.
In the Dub, when Yugi sees Yusei Synchro Summon Junk Gardna in the final duel, when Yugi says "Synchro What?", everybody laughed.
In the most high-pitch voice possible - it was almost impressive.
Jaden's epic use of the "bowman's salute", once you spot it.
Jaden: I'll see your Trap, and raise you with one of my own!
Literally seconds after Yugi finds that his Grandpa is dead, he's basically abducted by two dudes on a time-travelling motorbike, and when they drop him off half an hour into the past, he gets thrown into a metal railing. His face says it all, really.
"I've seen a lot of dragons in my time, but that really takes the cake." "And he probably ate it too." Yeah, it's cheesy. But it was funny.