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.
Ensemble Darkhorse: The Demon Sorcerors are very popular antagonists. It helps that despite having only a few episodes each (save Shendu), they all have distinct personalities and decent characterisation. Several are generally more popular than others, but they all seem to have some kind of individual fanbase.
Jade's Super-Powered Evil Side, the Queen of the Shadowkhan, only appeared in a filler episode in season 2, and was referenced a couple times in Season 4, yet she's incredibly popular. There are plenty of fanart of her and many fanfics where Jade turns again into the Queen (or was never restored back to normal).
Fanon: Ask the fandom for this series, and Jade and Hsi-Wu is the series enduring love story, when it was only (and barely) teased in at least two of the series episodes. Nevertheless, the amount of Fanfic for this couple is quite high, even by today's standards.
Foe Yay: Hsi Wu. It doesn't help that the only other closest thing poor Jade has to a love interest is Paco.
Jackie/Valmont fic is probably second in popularity after that couple. Followed by Jackie/Viper, Jackie/Finn, Valmont/Finn, and Valmont/Jade (with either child Valmont or adult Jade).
Fridge Horror: In 'Attack of the J-Clones', an evil wizard who is never seen again creates magical duplicates of the five members of the J-Team. These magical duplicates are flawed, but they are also morally good just like the originals. The evil wizard brainwashes the J-Clones into being evil, but in the end of the episode they are turned back to the side of good and fight alongside the J-Team originals. But after this, they are never heard of again. What happened to them?
Hilarious in Hindsight: A meta example. Jackie Chan and Julian Sands would later go on to play opposing characters in The Medallion (in fact several reviewers called it a live action version of the show).
Ho Yay: Uncle beats himself up over letting Tohru be taken by shadow khan and is willing to let himself be engulfed by dark magic to save him, as well as (in another episode) swallow his pride and call a psychic for help when he can't find the ingredient that will wake Tohru up.
Uncle (in front of phone): *casts Tohru wistful look* "For you...my apprentice."
Likewise, Tohru is very protective of Uncle and hates to see Uncle upset. And when Uncle returns to the team in "Samurai Ratso", he's positively elated and cries touched tears. Besides, in the same scene, tell me Uncle having their blowfish kiss to share the magic wasn't symbolic...
Finn, Ratso and Chow have a very close three-way dynamic. They're never apart, never show any interest in anyone outside their trio, always look out for each other...heck, when Finn decides to quit The Dark Hand and start his own crime syndicate, Ratso and Chow immediately quit too so they can keep working with him.
Ratso: "After you quit, we told Valmont he'd better give us raises, or we quit too!"
Finn (thrilled): "And now you guys wanna work for me? That is so c-I mean, that's cool."
Paco's starry-eyed devotion to El Toro seems a bit over-the-top. The fact that he seems to not have any parents and even travels with him doesn't help. On the other end, El Toro also does not help by referring to Paco so affectionately all the time. "Mi Pacito", indeed.
Jackie sees red and loses his cool only when Captain Black has been injured by the bad guys. Then he recklessly goes out for revenge.
Jerkass Woobie: Valmont and Shendu both become more sympathetic by season 2.
Launcher of a Thousand Ships: Pick a character - ANY character. Chances are that Jade's been paired up with him/her in the fandom at some point or another.
Ron the Death Eater: Jade is an interesting case, in that it's not actually her haters that do this to her. Rather she has a lot of fans who really liked her as the evil Queen of the Shadowkhan. There's a lot of fanworks that have her change back permanently.
The Scrappy: Jade got this at first, but familiarity helped to dull it making her either a Breakout Character or Creator's Pet depending on the viewer. At the least, any trouble-making caused by her interference she either fixed herself or managed to make her mistake into something useful, so she was rarely The Load. There were other times when she also played the Big Damn Hero whenever the other characters would go off on their own though haters simply see this as shoehorning. She also tended to be the most wily hero coming up with clever solutions the others never considered. Ethnic Scrappy Paco, however, is hated far more.
The Ice Crew was not well-received by viewers, especially when they replaced Finn, Ratso, and Chow in the last season. Ice probably gets it the worst because of the way he talks.
Tohru's Mother at least in her debut episode for treating Jade like a child, and being all around rude to Uncle (though at least Uncle was capable of firing insults of his own) and for initially berating her own son (i.e. scolding him for not owning a car and making her "walk in a typhoon" despite the fact that Tohru was holding an umbrella over her head keeping her dry while he was soaked).
Villain Decay: Valmont and his mooks are the bad guys in the first season, and a Shendu-possessed Valmont is the Big Bad for the second, but it sets in with a vengeance during the third season, thanks to the first two seasons draining all of Valmont's capital. Valmont's goons split after that, and Valmont became a washed-up has-been dreaming of former glory. In his last major appearance, he was nothing more than a gag villain who was accidentally mailed to Mexico. In the end of series episode, he's reduced to being a bus driver.
Notably, Valmont had been able to hold his own against even Jackie in hand-to-hand combat during their first confrontation. He has never displayed anything close to that level of combat since then.
The Dark Hand as a whole was introduced as a Nebulous Evil Organization worthy of the attention of the super-spy agency Section 13, and originally had many members and a wide range of resources and connections. By the end of the season its down to 4 men, Hak Foo making five the next, and eventually just becomes Finn, Ratso and Chow
The Shadowkhan and Dark Chi warriors suffer tremendously from this, to the point where they can hardly be regarded as much more than an inconvenient annoyance.
The Shadowkhan play with this a bit; they become a global menace in the 4th season as the ancient evil army of a demon Evil Overlord, and there are now several different tribes of them with unique abilities. On the downside, this makes the classic ninja-Khan seem Overshadowed by Awesome.
Hak Foo, too.
Tear Jerker: Season 1 gave us Lo Pei. Jade used the Rat Talismen to bring a statue of Lo Pei, the man who turned Shendu into a statue, to life. However, after he realizes that he's not the real Lo Pei, he sacrifices his new life to return the Rat Talismen to Jade.
They Wasted a Perfectly Good Plot: In season 5, Jackie retrieves another priceless artifact and runs into a group of his enemies from the season 2 filler episodes consisting of the pirate duo from Glove Story, the treasure hunter from Scout's Honor, the black market archeologist from The Deep Freeze, and the monk from The Lotus Temple. Only for Jade to save Jackie once again and while nothing fatal happens to them, they're never seen again.
Also in the season 3 finale, Dalong Wong revives Shendu in exchange for Shendu's power of combustion. Shendu cheats Wong by absorbing the power himself and also steals Wong's powers of Levitation and Heat Beam Eyes. Wong then summons Finn, Ratso, Chow, and Hak Foo, gives them battle armor and tells them to attack Shendu for backing out of his promise. It seems like we'll see either a 3 way fight between Jackie, Shendu and Dalong Wong, or at least a battle between Shendu and Dalong Wong, only for Uncle and Tohru to turn the dark warriors back to normal and take away the rest of Dalong Wong's magic.