These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
YMMV: Yu-Gi-Oh! GX
Accidental Innuendo: In the original, Edo (having the D-Hero deck), often says things like "the power of the D" or similar in reference to destiny. When "the D" is taken to be the OTHER one, some really hilarious accidents occur.
Ass Pull: It's amazing what you can do when the main character's deck is based entirely around fusion. Plus all the E-Hero support cards that are just completely useless in real life due to how specific they are. Ryo's initial Deck focused on a single monster and its Fusions, and getting the same results in a real-life Deck would take incredible luck.
For those attentive enough, the series is full of references to alchemy and tarot, including a Foreshadowing to the antagonist of the final season.
The duel in Episodes 153-155 appears to have been structured to mirror or strongly resemble a Jewish wedding, beginning with Magic Chronicle as Yubel's dowry and the ketubah (Jewish wedding contract) and ending with a "cracked glass" when Juudai manages to take back Super Fusion and join his soul to Yubel's, something he reveals only after the worlds start shaking apart and the window in Samejima's office cracks and shatters. With the exception of a couple of Juudai's more convoluted turns, it's actually possible to trace every single turn back to the ceremony, in perfect sequence. The resemblance even continues after the duel—in a Jewish ceremony, the ceremony is complete when the bride and groom retire together, away from the guests (represented in this case by Sho and Ojama Yellow). The German dub even adds a touch of its own, with Syrus commenting that "[Jaden] and Yubel are united among the stars".
Ho Yay: A moderately-sized plot point for season 3 is that Yubel (who is a hermaphrodite using male pronouns for "her"self; Juudai also refers to her as "he") believes that Juudai (who is male) loves/is infatuated with/spends too much time with Johan (also male). It's unclear if this is lampshading, or just YGO being YGO.
A special mention has to go to a piece of Ho Yay so blatant it borders on hilarious: while Yubel is utilizing Johan's body, she calls Juudai her beloved, tells him she will "show [him] the truth of [her] undying love," and tells him "aishiteru, boku no Juudai" ("I love you, my Juudai"). Seeing screencaps with subtitles taken out of context may be enough to drive some Juudai/Johan fangirls straight into hysterics.
Episode 147 features "Johan" calling Juudai "my beloved" (or, depending on your subs, "in just a moment I'll show you the truth of my love"). While everyone around them gasps, Juudai just kind of stands there with no reaction whatsoever. One Japanese-to-Spanish fansubber takes the nuance even further: because of the different words for "love" in Spanish, the line translates from Japanese to Spanish to English as "In a few seconds I'll show you the truth of my desire, Juudai, my love." Given the context, there really is only one way to interpret that.
Informed Wrongness: A Season 1 episode features the one-shot character Mitsuo/Pierre, a gambler who uses cards that rely on coin tosses to trigger their effects, and uses Second Coin Toss to redo the toss if he fails to get the needed result. Asuka declares that the only reason he's winning the duel with her is that he relies on Second Coin Toss to win his coin throws and without it he would have lost them all, and proceeds to destroy it and then attack for the win when he gets his last toss wrong. We're supposed to see Mitsuo as a cheater and a coward, but his strategy is perfectly valid and worked very well. The only reason he lost is that he didn't use his monster's effect to try and inflict 1000 damage to Asuka, if he had done so and got it right, he would have just won in two turns.
Jerkass Woobie: Cobra. All he wanted was to reunite with his dead adopted son, and he would no longer have any reason to be an antagonist if he met his goal. Amon wanted to create an idealistic world, and though he kills two people in the process (Echo and Ed), the former willingly sacrificed herself and the latter started a duel to protect the former, knowing the consequences of losing. Both are presumably killed by the far less sympathetic Yubel.
Camula may count, She's the Last of a race of Vampires that were wiped out hundreds of years ago by humans who attacked them unprovoked and she sealed herself in a coffin to survive and waited for eons to be freed. She seeks to restore her Race but she sacrifices The Souls of those she defeats in Duels to do so.
Lady Mondegreen: Oh 4Kids...their dub of episode 154 will forever haunt them. The filter voice they put on Yubel distorted her voice so oddly that, at one point, she ended up sounding like she dropped an F-bomb when she says fight.
Asuka/Alexis was a Deconstruction of Ms. Fanservice, she was annoyed by how people saw her as an attractive girl and wanted to be seen as a person and a duelist instead of just a pretty face. Many fans don't care since this gets in the way of Shipping, and other fans often use it just to bash her for being a "slut."
Moe: Rei, and her Maiden in Love monster from her first appearance.
Zane Truesdale (Ryo Marufuji) in the second season crosses the line after donning his Dark Kaiser persona when he electrocutes and almost kills his little brother Syrus (Shou) in a duel, never giving a damn about doing that, only about winning.
Amon when he sacrifices Echo and apparently kills Aster to obtain Exodia.
Yubel at every attempt in the 3rd Season with Jaden.
The Underground is less supernatural, but still incredibly disturbing.
One-Scene Wonder: For the dub. He may only have two episodes and is a minor character, but Marc Thompson's voice acting, the usage of the original series themes and cards, and the genuinely good duel he gave Jaden, make Dimitri far more memorable than a lot of other characters with larger roles.
Superlative Dub: Episode 18 and 19 with Dimitri, the copycat duelist. In the original Dimitri was just Dimitri and only decided he was Yugi towards the end of the duel, but in the dub Dimitri acts like he's Yugi all along. What really sells the episode though is the absolutely Narmtastic impersonation of Dan Green's Yami Yugi that Marc Thompson delivers, taking Green's Large Ham, cranking it up, and giving a few lighthearted jabs at his mannerisms and catchphrases. The dub also re-uses parts of the original dub soundtrack as further nostalgia fuel when Dimitri makes his moves.
Season 3, more so as it continues. Ryo's death may be the top.
From Season 4, Episode 178: Yubel being forced to attack Juudai head-on by Darkness. The look on her face as she's forcibly dragged across the arena an inch at a time is absolutely heartbreaking. Followed by a Crowning Moment of Heartwarming when Juudai takes her hand and vows "I'll get you back, no matter what!"
Fubuki screaming for Asuka after she's lost to Darkness.
From the manga, when Midori realizes she has to sacrifice the possibility of getting information on her younger brother Koyo's coma out of Reggie to prevent Judai from having to duel her, accompanied by a mental vision of Koyo telling her she's doing the right thing. She's unable to win, though, and collapses, comatose in front of Judai.
What was Yubel during the twenty episode absence after possessing Johan but before confronting Juudai?
Rogue card designer with a counterfeit Egyptian God? The whole thing resolves in one episode.
What were Judai and Yubel off doing after they fused? It's implied that Judai was gone for quite a while (enough for most people to think that he was gone for good), so what were they doing?
It's implied that they were going to go and kick the Light of Destruction's ectoplasmic patuckus, making this closer to Offscreen Moment of Awesome given that it wasn't actually shown (probably because it didn't involve card games).
While the concept wasn't really wasted, the history of the Sacred Beasts/Phantom Demons is not explored at all, such as how evil versions of the God Cards were created and how they got sealed under the island.
It's mostly based on the video games but a lot of people would prefer if Rei used Lightsworns instead of her current deck considering how much better the deck is.
What an Idiot: Why didn't anyone just remove/break their bio-bands during the Dimension World arc?
Because they can't. It's mentioned at one point that they've tried and the only way they could would be to cut off their arms.
The "Bio Bands" and "Survival Duels" in the dub were known as "Death Belts" and "Disclosure (seems benign, until you realize it's a pun on the Japanese pronunciation of death) Duels". (called Dis-Duels in Tag Force 2). God knows why the faculty weren't tipped off to the true nature of Cobra's actions when he pitched the idea in that version.
That's easy. Because the Disclosure Duels had already been held in West School where Cobra worked before and nothing had gone wrong there. O'Brien even mentions that the effects are different.
Banner's German accent.
While the symbolism of the name is lost, it could be argued that Nightshroud is a more impressive name for a villain than simply "Darkness".
The D, in the Japanese named "DD" for "Destiny Duelist". The dub established "The D" was an alias and gave him the proper name "Kyle Jables", take from Kyle Gass and Jack Black of Tenacious D.
A bit of a mean one that nonetheless works — the monkey duelist being trained by Kaiba Corp in Season 1 was named "Sal" in the Japanese version, meaning "Super Animal Learning". The dub renamed it "Wheeler", after one of Kaiba's favorite insults for Joey, "dueling monkey".