Within moments of his reveal, Reiji Akaba has been christened by many as "Hipster Kaiba", especially when he wears that trendy hoodie while eavesdropping in episode 9. Just take one look at him and no further explanation is needed.
Yuya has been nicknamed "Tomato Head" by many. Once again, such a name needs no explanation.
Posts with Yuya being sad, uncomfortable or upset are often tagged as wilting/rotting tomato, and posts of him injured are "bruised tomato".
The Dark Duelist Yuto is also referred to as the Goth Duelist, Edgeplant, Edgeyuya or Dark Yuya. As of Episode 35 and the duel splash screen that renders his name as "Ute", the less-serious nickname "yoot yoot" has also been making rounds.
Immediately after his appearance without the helmet was revealed, fans started calling Yugo "Banana Head" due to his bangs, or "blueberry-banana" in reference to his entire hairdo.
The alternate Yuzus are known as Fuzu (Serena), Edgeyuzu (Ruri), and Synczu for the as-yet unnamed Synchro variant. Yuzu herself is usually named "the citrus" (which her name literally means), to go with the tomato.
Futoshi is universally known throughout the fandom as "Shivers Kid." Largely because no one remembers his name or anything about him besides his catchphrase.
The Raid Raptors/Raidraptors are called "RuriRaptor", or "RaidRuris" by the fans, due to Kurosaki's obsession of rescuing his sister. Kurosaki's picked up the nickname of "the imoutoman" in some circles, for the same reason.
People has nicknamed Yuya and his counterparts from each dimension the "Yu Squad"
Whenever Yuya or his counterparts use their Superpowered Evil Side, everyone calls this their "Berserk Mode" or "Berserker Mode".
While it's not normally obvious, as soon as Reiji starts hamming it up, anyone who watched the previous series will likely get IV flashbacks. Before them, their seiyuu voiced the minor character Dick Pitt, one of the Dark Signer Drones from 5D's.
Name's the Same: Hokuto Shijima's dub name is Dipper, which has gotten many comparisons to another Dipper.
Real-Life Relative: The seiyuus of Yuto (Manpei Takagi) and Yugo (Shinpei Takagi) are twin brothers.
Teasing Creator: The showrunners seem to know exactly what will annoy the fans and lampshade or address it. Examples include:
Yuya's Ass Pull of getting his Pendulum Monsters mid-duel is considered as such in-universe.
Futoshi, who is considered The Scrappy by many, and is a wee bit of a Fat Idiot, usually gets a few derogatory comments thrown his way.
Kyuando is another scrappy who earned attention from the creators. While Yuya's other opponents during the Qualifying arc (Michio, Mieru and Gongenzaka) appear in the second opening, Kyuando is left out.
Your Size May Vary: In episode 24, Hidekazu Ebina (the episode's animation director) said that he intentionally made Yuto taller than Yuzu despite that he's supposed to be shorter than her. His reason was that this was supposed to give Yuto's exposition a sense of seriousness.
Yuya has used more Extra Deck summoning methods than any other previous characters from any previous series.