Season 1 (Seven Stars arc): It's revealed that the school was built over the hiding place of 3 powerful, Evil Counterparts of the Egyptian God cards and that its purpose is to raise students strong enough to defend them (the gate sealing the cards can only be opened if its 7 keys are won in a duel). Naturally, Juudai and co. are entrusted to guard said keys from the Hidden Agenda Villain's henchmen.
Season 2 (Society of Light arc): Takuma Saiou, possessed by the Eldritch Abomination the Light of Ruin, comes to the school to recruit members for his cult, the Society of Light. Juudai meets his Anti-Hero counterpart, Edo Phoenix, whose best friend and manager Saiou uses to brainwash his victims by putting a Defeat Means Friendship spell on Edo's deck.
Season 3 (Dimension World arc): When things started to get... strange as the show headed down a slow but steady path from lighthearted comedy to Neon Genesis Evangelion levels of disturbing, angst, and creepiness. Juudai becomes close friends with Johan Andersen when students from Duel Academy branches around the world come to compete in a tournament. When an unknown Hidden Agenda Villain's actions get Johan Trapped in Another World, Juudai becomes dangerously obsessed with finding him. His journey eventually leads to: the apparent deaths of all of his friends, his discovery of his Superpowered Evil Side and the past life of his Reincarnation, and meeting his Stalker with a Crush Yubel, a horrifying card he had as a child that harmed anyone who defeated him, prompting him to launch her into space. Now she's back and she's not too happy about that...
Season 4 (Darkness arc): The Story Arc that was made on drugs... okay, it was technically just rushed because the protagonist's voice actor apparently had to leave early, but that alone does not account for how Mind Screw-y the once relatively normal Gaming And Sports Anime And Manga suddenly became. Each character's individual Coming of Age Story as they choose careers and carve paths for themselves (Manjoume wants to make a name for himself in the Pro League without relying on his family's fame or fortune, Asuka has to choose if she'll accept a job as a teacher in America...) is interwoven with an Assimilation Plot executed by the personification of all despair and Darkness, and the resolution of the mystery of Fubuki Tenjoin's Enemy Within introduced in Season 1. This season was not dubbed
Adults Are Useless: Prevalent in Season 3 and even Lampshaded. The students resign themselves to the fact that the remaining teachers have mentally lost it and won't be of any help. Principal Samejima may be a Deconstruction, as constantly burdening his students with the task of defending the Artifact of Doom and saving the world causes in a great deal of inner anguish.
Anti-Hero: Edo Phoenix was designed to be the Anti-Hero to Juudai's hero, using a Destiny Hero deck that countered Juudai's Elemental Hero one. It's even lampshaded when Edo jokingly notes that they (he and Kaiser Ryo) are heroes too, but they're jerk heroes. Right before killing the mooks they were threatening for information.
Awesome, but Impractical: Quite a lot of the duel disks in the third season, including The Supreme King's (which spins like a buzzsaw), Johan's (which appears to be ... made of giant razorblades), and Yubel's (which is actually an extension of her arm). The question many a cosplayer has moaned over is: How do you actually build and use any of these?
Ax Crazy: Yubel, until the end of the third season.
Back To Back Bad Asses: Sho and Kenzan after they settle their differences and start working as a team against Ikazuchimaru and Kourimaru. Kenzan does another one with O'Brien as they hold the line against Duel Ghouls long enough for Johan and Hell Kaiser Ryo to open a portal to deliver the "Rainbow Dragon" card.
Badass Biker: Saiou on a Yamaha is pretty damn epic. Then Judai tries it and crashes.
Badass Longcoat: Several characters wear long coats as part of their school uniforms, as do a couple of villains.
BFS: In the second episode of season 2, one character plays Gilford the Legend and equips him with four different swords, each of which gradually increase the size of Gilford's already largish sword. Ultimately the sword ends up about five to six times as long as he is tall. Heavily lampshaded in the English dub.
Bi the Way: Various characters assume Juudai has something going with Johan (and O'Brien also wonders about Juudai and Jim), and the hints are spread pretty thickly on the ground. Meanwhile, Juudai's "girlfriend" turns out to be a hermaphroditic duel monster, and before she turns up, he does spend some time blushing while in close proximity with a (fully female) Duel Monster.
Book Ends: Juudai's adventure in Duel Academy started by meeting Yugi, the King of Duelists himself, and giving him the Winged Kuriboh card. It ended by Juudai going back in time and dueling Yugi himself as his true Graduation Duel. Juudai lost, but not before realizing that the whole point of the duel was to return his lost passion for dueling.
Brainwashed: The members of the Society of Light and Fubuki in Season 1, as well as Yubel. In some cases also ties into the next trope.
Jaden: "Man, I could sit here and have flashbacks all day!"
In one episode in season 3, Jaden asks Syrus to go find some water, for some reason, while Jaden duels against someone. After the duel, Jaden says the water isn't needed anyway, to which Syrus just says "Aw man. And I've been carrying that water for three whole episodes."
"The sooner I beat you, the less bad dialogue I have to hear."
Broken Aesop: The copycat duelist Dimitri stole Yugi's deck and challenged Jaden to a duel with it. He lost, but allegedly it was because he didn't put any heart into his deck. There is a Truth in Television...well, gameplay anyway that there is very few wrong ways to construct a deck and that if you do build your deck your own way, you can have fun with it and use whatever combination of strategies that best suit your style of play. That lesson would have been great to teach in this episode. However, the events of the episode display a stark contrast. Dimitri was doing wonders with Yugi's stolen deck. Despite not having the heart of the cards, Dimitri was sure using it very effectively enough to strengthen the argument for netdecking. This can cross over into Family Unfriendly Aesop as well; teaching duelists that some strategies will always work better than others.
The Cameo: Several of the original series characters, among them Pegasus, Kaiba, the Paradox Brothers and Yugi's grandfather. Also, Yugi himself in the first episode, although his face isn't seen.
Then Yugi shows up again both as his faceless older self then His younger self As Juudai's last opponent of the series
The Casanova: Fubuki. He even has a little black blue book. In one of the last episodes of Season 1, Chazz/Manjoume Jun tries to be this. The English version of the episode is even named "Chazz-anova". He subsequently fails at beating Asuka in a duel and thus (through some strange logic that doesn't even apply in most anime) win Asuka's heart. Instead, he loses while having all the Spirit Keys in his possession and thus lets the Sacred Beasts/Phantom Demons free.
Catch Phrase: Lampshaded in the dub at least, during Aster and Jaden's third duel, when the former summons Destiny Hero Dogma, Jaden's scooby gang reacts with shock, saying things like "Aww, man!" (Syrus), "Great Scott!!" (Bastion), and "Sam Hill!!" (Tyranno). Then Alexis asks why she doesn't have a catchphrase.
"Great Scott!!" isn't Bastion's catchphrase, but it is a catchphrase. One of his more common phrases is "Good show."
Character Development: More or less everyone gets some character development, but most noticeable are Juudai's, Sho's, and Manjoume's development.
Chaste Hero: Judai. Debatable as to whether he's oblivious or uninterested.
Chekhov's Boomerang: The Phantom Demons/Sacred Beasts that constantly seem to be sealed up or lost and then suddenly be broken out and used again. And then ultimately never mentioned again after their last use, with it not even being made clear they were sealed again.
Chekhov's Volcano: Averted. The volcano is featured prominently in far-off shots and is the site of several duels. But it never erupts.
An interesting incidence of color-coding: there are two boys in GX, and only two, with brown hair and brown eyes (Juudai and Fubuki). Juudai has light brown hair/eyes, and is the embodiment of the Gentle Darkness (of creation). Fubuki's hair and eyes are dark, and in the first and last seasons, he appears as the Darkness of Nihility, which goes around destroying things.
Combat Commentator: It's Yu-Gi-Oh, so of course someone has to be there on the sidelines to make sure the audience didn't miss anything. In some Season Four duels where there's nobody left alive to commentate, the duelist currently representing the protagonist side of the fight will serve as his own commentator.
Continuity Nod: The series first tag duel is played against the Labyrinth Brothers, who were also the opponents in the first tag duel featured in Duel Monsters. In Season 2, Sho and Kenzan tag duel two opponents on top of the same building that Yugi and Kaiba did in the original, and in Season Four, the dock Juudai and Johan meet on in Domino is the one Yuugi and Jonouchi dueled on in Battle City of the original YGO. Then there's the various nostalgic appearances of Black Magician and other signature monsters of the Duel Monsters characters, including a replica being offered as a prize in Season 4.
Dangerously Genre Savvy: Saiou makes Yu-Gi-Oh! history by ordering a Brainwashed minion to activate his Kill Sat and destroy the world before defeating the protagonist in their duel! In fact, he wasn't going to bother dueling Juudai in the first place, because he managed to trick him into giving up the MacGuffin. He only did duel Juudai because he absolutely had to, and began said Kill Sat firing the moment Neos was out of the way.
Defied Trope: When Juudai faces down Yubel, he admits that there's no point giving Yubel what we call a Kirk Summation. (For the record, Kirk Summations practically never work even when they are given...)
There is an art meme on Deviantart that mentions this. "NOW DRAW MISAWA BEING IGNORED LIKE HE ALWAYS IS LOL!!"
Department of Redundancy Department: Drillago's attack name is Drilling Drill. In addition, there's a trap card called Entry Forbidden! No Entry!. The dub shortened this to No Entry!, which was actually a well-received change.
Don't Explain the Joke: In the dub, while Jaden is dueling Sartorious, Jaden not only tells an incredibly lame joke, but he explains it immediately afterwards, making it even less funny than it already was. It seems 4kids was aware of this, as Aster points out the failness of the joke immediately after. SO WHY DID THEY WRITE THE JOKE IN THE FIRST PLACE?!?
Jaden: You said I was the puppet, but it looks like you're the dummy. Get it? Puppet, dummy?
Syrus: Oh, yeah. Good one, J.
Aster: A joke's not funny when you have to explain it.
Double Entendre: Most people, when they summon a monster, say "I summon (insert monster's name here)". Johan, on the other hand, does things like "Rainbow Dragon! COME OUT!" (And yes: "come out" means in Japanese exactly what it means in English).
Dub-Induced Plot Hole: Rei may have passed for eight years old in the first season, but not in the second.
Dub Name Change: Being dubbed by 4KidsEntertainment, nearly every character. For exceptions, we have Jim "Crocodile" Cook, the distinctly Japanese-sounding villain Kagemaru, and his underlings Camula, Abidos, Titan and Amnael. Princess Rose, Prince Ojin, Yubel, The Alien of Light, Alice, Doctor Collector and The Supreme King also retain their original names (in Supreme King Juudai's case, the perceived "name change" is actually just a translation, with the word "Haou" meaning "Supreme King"). Though Americanization runs rampant, there are some odd cases of reverse Americanization such as Jim's crocodile Karen becoming Shirley and Sara becoming Yasmin. To avoid confusion since both names for a given character may pop up, here's a list.
Evil Hand: Yubel somehow alters or transplants her own arm onto both Martin and Amon.
Evolving Credits: The credits in the first part of Season 3 featured Juudai recalling events from previous seasons as he stands back-to-back with Johan. The latter part of the season after Johan's disappearance features Juudai recalling his memories of Johan, standing back-to-back with a ghostly, transparent Johan.
Executive Meddling: Both the anime and the manga had the tail end of the series rushed due to the execs wanting to push out the newer YGO series (Yu-Gi-Oh 5D's and ZEXAL respectively).
Expospeak: As in the original series, for the benefit of viewers, duelists have to describe the effects every time they play a card, even one they've already played... sometimes against the same opponent or even in the same episode! Not surprisingly, the dubbed version uses Lampshade Hanging, with the opponent frequently responding, "Thanks, but actually, I already knew that!", or some variant thereof.
Manjoume: also Kaiba, mostly in how he dresses, talks, and some identical dueling strategies. Oh, and they're both from filthy rich families who are the top of their individual corporate worlds, which they actually attempted to pressure Manjoume into doing with the dueling world during the first season.
Edo: A third expy of Kaiba, in his Rival status and generally feeling he's superior. The fact that all three characters go through some form of Break the Haughty cannot be a coincidence.
Johan, who is, quite undeniably, an Expy of Juudai!
Johan also looks a bit like Nagisa Kaworu, and even serves a similar role (shows up late in the show, befriends the main character immediately and then later turns against the protagonist). The main difference is that Johan didn't turn against Judai in the first episode he appeared in.
Also worth noting is the fact that hey-wasn't-he-a-main-character-once Misawa has a couple things in common with Ryo Bakura, including getting British accents and keeping their original (and distinctly Japanese-sounding) last names in the dub.
First Name Basis: Sho begins calling Juudai his given name, rather than "Aniki" after he loses faith in him during Season 3. He reverts back to "Aniki" in Season 4. Manjoume tells Asuka she can use his given name, Jun, instead of calling him by his family name. She is the only person he ever makes this offer to.
Highlighted in this collection of clips. Yes, that's the real dub's dialog, not an Abridged version.
Gecko Ending: The English dub ends one episode short of the end of Season 3 and insinuates that Jaden sacrificed himself to stop Yubel. Given where Season 4 went, some argue that this is a better ending.
Is the infamous Juudai/Johan ship actually canon? There's a scene during Ryou vs Yubel in which Johan!Yubel either (depending on your chosen subtitles) calls Juudai "my beloved" or states "In just a moment I'll show you the truth of my love," but although Juudai indicates he believes he's actually talking to Johan, he doesn't react to the pet name—even though Chronos, Shou, Taniya, and Misawa all gasp and give Juudai "did he just say—?!" looks.
This can be debunked however, as Johan says a very similar dialogue of "showing love" to Ryou right before Juudai's appearance. Juudai also seems to register Johan as being possessed by Yubel, as demonstrated by his calling for Johan to regain control of himself.
The Gift: A recurring theme is that the better someone is at Duel Monsters, the more painful their fall will be.
Giving Someone the Pointer Finger: Juudai's trademark catchphrase is the English word "Gotcha!" accompanied by pointing with his index and middle finger. In the dub, it's "That's game!"
Good Colours Evil Colours: Not just the dorm colors; in defiance of the "black = evil" trend in media, members of the Society of Light all wear white, probably because of the "White = Death" trend in the East. The West may also see all-white as related to madness and/or zealotry, two qualities in which the Society of Light is not lacking.
Graduate from the Story: Juudai and the rest of the main cast graduated from Duel Academy at the end of the series, with Asuka giving the graduation speech. There was also a graduation ball after the ceremony that Juudai did not attend in order to get packing and leave early.
Brilliant, but Lazy: Of course, it's implied he fails the tests solely because he falls asleep during them. As for being the top duelist, well, he practically has the same power of luck that Yami Yugi had with the Millennium Puzzle...except without the actual Millennium Puzzle.
Hate Plague: Given to Sho, Fubuki, Asuka, Kenzan, and Manjoume toward Judai temporarily in Season 3.
Hermetic Magic: Amnael's Emerald Tablet which he used to trap Fubuki's, Manjoume's and Asuka's souls as well as Saiou's Tarot deck. Then there's Fujiwara's ritual to summon Darkness, resulting in the Abandoned Dorm.
Hide Your Gays: Averted in the third season, where two separate people (three, if you count Sho ranting about Johan in the previews) assume Juudai may have an interest in guys, to the point where Yubel possesses Johan in an attempt to make Juudai surrender to her. The actual 'ship that's most hinted never happens (that we know of—see Getting Crap Past the Radar above), but Juudai ends up with someone who's half-male anyway. There really isn't any smoke without fire in this case.
Special mention goes to an absolutely trope-smashing line from O'Brien in Episode 139: "Jim, was there . . . anything between you and Juudai?"
And another from Yubel, talking to Juudai about Johan, in Episode 154: "You truly prefer that boy over me? Even the love you gave me is his now?"
Hostage for MacGuffin: Saiou holds Edo hostage, threatening to kill him if Juudai doesn't hand over the Kill Sat keys. Juudai, in what's probably his most Genre Blind and idioticmoment ever hands them over, then challenges Saiou to a duel. Which the Genre Savvy villain declines, until outside forces (Neos) force him to duel.
Earlier, a villain holds Sho hostage, causing Ryo to lose so that Sho's soul is spared.
Hot for Student: Nurse Ayukawa for Fubuki. She his seen alongside most of the female students in Fubuki's rabid fangirl cheering section. The first Tag Force game expands on this. Ayukawa will only agree to be the player's partner if they bring her Fubuki's autograph.
Scientist: Please! That would be completely unrealistic. His helmet reads his mind and talks for him.
Idiot Hero: Juudai, to a T. This trope applies well in his case only up to the halfway mark of Season 3, when his deconstruction begins in earnest. By the time Season 4 rolls around, he can be described as an interesting combination of The Messiah and the Ineffectual Loner—in the sense that while he still cares for his close ones, he makes efforts to distance himself somewhat from them in order to allow them their own growth, away from his influence. During this time, most of his interventions are generally marginal and only meant to nudge the other person in the right direction, not whip them around in what fashion Juudai sincerely (but also selfishly) wanted them to take.
Self-Parody: With the dub however, it's clear by the time Season 3 came that the writers were getting bored and started poking fun in their own ways. As noted at the top of the CMoF page, the dialogue in some episodes would not sound out of place in Yu-Gi-Oh! The Abridged Series, and 4Kids is known to be aware of the parody's existence so this may well have been on purpose.
Invincible Hero: Juudai, who's lost three times (out of his 73 duels) throughout the whole series. Ironically becomes one of the reasons for his fall to The Dark Side.
Averted in the manga, where Juudai actually loses the first major tournament he enters. He doesn't even make it to the final round against Kaiser; Manjoume knocks him out in the semi-finals. Hey, if it keeps him from going evil, it might have been worth it in the long run.
This trope hits hardest during Judai's final duel with Darkness: despite having a near-broken deck, Darkness plays rather badly compared to the three final bosses who came before him.
I Just Want to Be Normal: Juudai gets rather tired of having the responsibility of saving the universe from evil. He just wants to play a card game. Of course, he eventually accepts that he isn't normal and decides that's not so bad after all, since it means he can actually help other people for a change, instead of being a selfish brat.
Invisible to Normals: Duel Spirits, though the definition of "normal" in this case isn't ever really clarified beyond "not able to see duel spirits".
"Just Joking" Justification: for the Genre Savvy, Johan's fake summoning of Rainbow Dragon in Episode 106 is funny; for the cast, his seeming mockery of something that is Serious Business is enough to cause shouting, anger, and general uproar. Johan even lampshades it by giving a large grin and announcing that he's "just kidding."
Just Smile and Nod: Used word for word in the dub with a character's delusions that he's actually Yugi since he stole his deck.
Karma Houdini: After spending an entire season manipulating, torturing, possessing, and killing people (not to mention turning the guy she loves completely batshit insane), Yubel...gets the guy for all eternity. Which was what she was after the entire time, since all she really wanted was for him to honour his promise to love only her for all time. Sure, we don't know why she went so wacko in between their lives (she was sane in their first life, after all) but she was not entirely in control of what she did.
Though his crimes don't even begin to compare to Yubel, Franz from season 2 episode 33 counts. He stole a copy of the Winged Dragon of Ra and hospitalized three people and Pegasus still let him keep his job.
The real Karma Houdini is Kagemaru. He wasn't possessed or controlled by anything. He made all of his own choices out of not wanting to die and what happened to him? Nothing. No punishment except the old age he already suffered from.
In short, Now the fourth season will never be dubbed.
Which introduces a Dub-Induced Plot Hole when 4Kids dubbed the recent movie since the dub makes it look like Jaden sacrificed himself to save everyone which leads some people to wonder how did he come back and why is he carrying around Banner's cat.
The Knights Who Say Squee: When Juudai meets Yugi again in the final episodes, he is nearly awestruck. At this point, Juudai had saved the world four times and could probably destroy it himself if he felt like it. But then again... it's frickin' Yugi!
Limited Wardrobe: Even if the students who wear uniforms are considered exceptions, there are still: characters who aren't students, like teachers, who wear the same clothes; students like Manjoume and Edo who don't wear uniforms but still wear the same clothes; and students, like Kaiser, who graduate but continue to wear their uniform!
Lampshaded by Edo, who actually has a whole closet full of clothes. They're just all identical.
Manjoume literally wears the same clothes: it's made fairly plain that his black North School uniform is the only one he has. And he never washes it. Ew.
Johan has one main outfit, a modification of the Obelisk Blue uniform ... which he wears before coming to Duel Academia, and possibly even before starting at North School (which has a different uniform to begin with).
Literal Genie: Yubel, who grants Professor Cobra's wish of being reunited with his son after he fails to complete his end of the bargain...by killing him. Overlaps with You Have Failed Me, but it's doubtful Yubel would have spared him either way.
The Magic Poker Equation: This is apparently not only an inherent magic power some have, but a skill you can learn, and more than one duelist sold their soul to a Duel Monsters spirit to gain this power.
Magic Skirt: In spite of their incredible shortness. This would be the girls' uniform, by the way.
Meaningful Name: An interesting example is Juudai's given name. The kanji it's rendered with translate as "teenager," but a different set of kanji with the same pronunciation mean "warrior"—reflecting first Juudai's personality in the first portion of canon, and then the role he takes later on as the universe's defender. (And the fact that his signature monsters are Warrior-Types.)
Meddling Parents: Juudai's parents, who erase his memories of Yubel, which—although they have no way of knowing it—is part of what drives her insane.
Merchandise Driven: To a point even fans of the original series complained. Juudai's deck uses an archetype built entirely around fusion, so in any given match, Juudai is likely to either introduce a new Elemental Hero, or just fuse a different combination of Heroes to make one. While Yuugi has only had 2 of his cards be cover cards (shown on the packaging, and usually one of the rarer cards in the set) in a booster pack, Juudai has had 5.
Nested Mouths: Uria and Saint Dragon have different forms of this.
Never Say "Die": The dubbed version of Season 3 replaces all references to death with awkward-sounding term "sent to the stars", though death was still heavily implied. They also kept all implications of Ryo's fatal heart condition, surprisingly. This was probably helped by the fact that none of Juudai's actual friends were really dead anyway. Amon, Echo, and anyone else who Juudai didn't care for? They're dead..
Ryo does actually die; his heart actually stops. But he just reappears in Season 4 alive but still with his fatal heart condition, with no explanation given as to how he's alive even though we clearly saw him die in the last season.
Official Couple: Amon and Echo are the first characters in the franchise to outright profess love for each other, beating Yubel and Juudai by a few episodes.
Unlike Amon and Echo, though, Yubel and Juudai do both actually get out an "I love you" (or, in Juudai's case, "Your love will be mine forever!" "Yes.") instead of just referring to their affection as an established fact.
Oh Crap: Juudai's reaction upon realizing he's dueling Birdman to the death in the alternate dimension and that the pain is real. One fansub renders it as "Shit, I'm going to die".
Old Master: Samejima, the sensei of a dojo that teaches Cyber-style dueling. Ergo, Ryo's old mentor.
Only I Can Kill Him: This is lampshaded repeatedly in Season 3, where other characters step in when Juudai tries to duel Mooks and remind him that he has to save his strength to face the person pulling the strings.
One Turn Kill: Saiou against Ojin in Season 2. Actually, he won before his first turn, causing Misawa to declare it a "Zero Turn Kill". Manjoume pulls off a more traditional example against a zombie student in Season 3.
Only Known by Their Nickname: "Kaiser" Ryo Marufuji, whose first name is barely ever mentioned. Not so in the dub. Does he even have a nickname there?
Out of Focus: Pretty much everyone whose name isn't Juudai, at least once.
Papa Wolf: Of all people, Medici/Crowler slips into this during one arc. He instantly steps in to duel a vampiric enemy saying something alone the lines of "What kind of teacher would I be if I allowed my students to be harmed?" Despite losing, it was still one of the few truly good things he does in the series.
Paper-Thin Disguise: There was apparently a sale at the generic gray cloak shop during Season 3. Asuka also fails to recognize her brother in Season 1, despite his only disguise being a mask.
Parental Abandonment: Hayato's father is the only one we ever see or hear mentioned in the series; the other closest thing to a parental unit the main cast has is Manjoume's much older (and politically and industrially successful) brothers. In fact, it was Juudai's Parental Abandonment that gave rise to the seeds of his obsession with dueling. That led to Yubel being overprotective of him whenever he lost and then he sent her into space in a hopeful attempt to get her the powers of the Gentle Darkness.
Punny Name: Copious amounts in the dub, though the original isn't devoid of it. Including most episode titles.
One such name is "Howard X Miller"—a reference to "milling," a strategy in trading card games wherein you win by making your opponent run out of available cards.
Yubel's name may be a Japanese pronunciation of the German "juwel" (pronounced "you-vell," with b/v pronounced the same in Japanese), meaning "jewel" or "gem". By itself it's nothing, but it's pretty funny when you consider that she considers the owner of the Gem Beast deck to be her greatest romantic competition.
Also consider that Yubel's name can be related back to both "Jubel", meaning "happy", and "Übel", meaning evil. "Happiness from evil"...?
Put on a Bus: Hayato leaves to work at Industrial Illusions at the end of the first season (cameoing in Season 2); Misawa leaving to work on a theory in Season 2 (returning in Season 3, only to get Put on a Busagain). Possibly even Fubuki between Season 2 and 3 (returns with no explanation after Duel Academy is transported back from the alternate dimension in episode 131, only to be 'killed' off).
Real Life Writes the Plot: Pot of Greed was used during nearly every episode of the first two seasons. Then it was banned in real life, and the duelists in the show stopped using it too.
Reverse effect example in the Anime, Part of Judai's Deck theme involves fusion, after that more of the characters in the show start to use it, then the overall game started involving more and more fusion and cards that focus on teamwork.
"The Reason You Suck" Speech: Juudai gets his share of these having to do with his lack of serious motivation, first from Edo, then Saiou/Sartorious, then constantly in Season 3 until he goes over the edge.
His duel with Brron is full of them, mostly from his friends.
Remember the New Guy: Fujiwara and Sorano in Season 4. It's lampshaded for Sorano when someone comments to Kenzan that Sorano is "that guy you hung out with almost every day." Fujiwara, on the other hand, who repeatedly says things like "I've been here for the last three years!" and "You must remember me, we've been best friends all this time," was actually only hypnotizing people into thinking they knew him.
Duel Monsters is on par with Politics and the Economy. We find this out from the very successful Manjoume Politics and Finance brothers, who want Jun to form the third pillar for World Domination. Also, Duel Physics.
Shoot the Dog: When Edo's about to win their duel, DD reveals that his monster has his father's soul trapped inside, trying to scare him out of attacking. Partly because his father asks him to free him, and partly since he's the Anti-Hero, it doesn't work, and Edo attacks.
Shonen Upgrade: Juudai's Neos Deck in Season 2, his powers as The Supreme King in Season 3, and his merger with Yubel. Ryo's Cyberdarks also count.
Shout Out: Just about every single Elemental Hero Juudai uses is based off of a comic book superhero (with Elemental Hero Neos being based off of Guyver as the only exception), while almost every single Destiny Hero is based off of a British hero (or, in some cases, hero/villain — Destiny Hero Double Dude Guy, for example, is notably based off of Dr. Jekyll and Mr. Hyde).
Similarly, Sho's Solidroid monsters from the manga are totally Getter Robo and his anime Super Vehicroid Stealth Union is a clear reference to GaoGaiGar.
The Supreme King's outfit, is quite similiar to Lelouch's Zero Outfit in Code Geass. The color scheme and the cowl that goes with it is too similar to be a coincidence.
Ruby Carbuncle is based on the Carbuncle summon from the Final Fantasy series.
Juudai's Defender Hero Trap Card from the manga features a figure that looks identical to MegaMan.EXE, protecting a figure that resembles Iris.
There are a lot of similarities between GX season 3 and a Super Nintendo game called "Illusion of Gaia." Just a few of them (listing them all could take a page all its own!):
General Freed > Freedan, the Dark Knight (whose armour resembles The Supreme King's)
The Light of Destruction makes Yubel evil > The Light of Ruin turns men into twisted creatures, reflecting the darkness in their hearts.
Juudai and Yubel fusing in S3 and going to fight the Light > Kara, the "Light Knight," and Will, the "Dark Knight," fuse together to fight the Comet of Destruction that brings the Light of Ruin.
Juudai lives forever > "I am Freedan, the Dark Knight. I am eternal."
The Supreme King and Juudai are actually the same person > Will and Freedan are actually the same person.
Juudai and Johan can see spirits -> Will and Kara (who swears she feels like she met Will before) can see spirits.
The Jeweler Gem has a special gift for "the chosen one" who collects all 50 Red Jewels
The location for Juudai vs Yubel strongly resembles the battlefield for the Fused Knight/Shadow vs Dark Gaia (the embodiment of the Light of Ruin)
Dark Gaia and Light Gaia both bear a resemblance to Yubel
One of Supreme King Judai's strongest monsters is out-right called "E-HERO Dark Gaia".
In the first save point (all save points appear to be in outer space): "Only the chosen one of Darkness can see this space."
There's a mysterious character—the only one with no backstory, as it happens—named "The Jeweler Gem."
The game begins and ends in a school classroom.
The character "Lilly" resembles Johan in appearance.
Some settings in the Freejia/Diamond Mine section of the game strongly resemble settings in Dark World.
Other settings in Freejia resemble the street Johan's on in the flashback with Tom.
And, if you want to prod more shout outs out of her, some of the names of her monsters' attacks include "Rondo of Death" and "Bloody Spiral."
Asuka's foil is named Rei. Also she disguised herself as a boy with last name being Saotome
In the manga, we have two characters who are usually just referred to as [[JAG "Rabb" and "Mac Kenzie" (or just "Mac")]]. The fact that they're both pretty good at what they do just makes the reference even more obvious! Albeit their first names are different, and they don't have quite the same personalities either.
Sparkling Stream of Tears: Yubel, during her duel with Juudai, when she asks how she's supposed to survive if he doesn't love her. She also cries facing Amon.
Spell My Name with an S: The most obvious example is the extended vowel debate that rages in all three Yu-Gi-Oh shows (Yuki/Yuuki, Judai/Juudai, Tenjoin/Tenjouin, Yusuke/Yuusuke), but GX has a couple of interesting and unusual examples outside of this...
Is it Johan Andersen, Johan Anderson, or Johann Anderson? All three spellings have been used in official Japanese merchandise or materials, and all three are technically correct spellings, varied by country ("Andersen" is Danish/Norwegian, while "Anderson" is Swedish/English, with "Johann" being the German variation on the Scandinavian "Johan").
Yubel's name is not Japanese in origin, and because her name is only ever spelled onscreen in katakana, the question isn't the spelling of her name so much as the name itself. "Yubel" could be the Japanese pronunciation of the German "juwel" (pronounced "you-vel"), meaning "jewel" or "gem," or a correct pronunciation of the Swedish "jubel," meaning "joyful." Nobody actually knows.
Third-Person Person: If a character refers to Manjoume without the -san honorific, he's likely to correct them with "Manjoume-san da!" which, loosely translated, means "That's Manjoume-san to you!" This is retained in the dub, where he insists he be called "The Chazz".
Also an instance of Punny Name, since his nickname in the Japanese show is "Manjoume Thunder," with "Thunder" being pronounced sandaa.
Triang Relations: Possible Type Seven. Yubel loves Juudai, Juudai loves Yubel, Johan appears to have something of an interest in Juudai, and Juudai has enough of an interest in Johan for Yubel to assume the boys have become lovers in her absence.
Zettai Ryouki: Absurdly short skirt and Grade E boots, which is absolutely ridiculous compared to the guys' Badass Longcoats. If Kaiba had any say in his school's uniform, he cannot be called a-sexual.