Awesome Music: That intro. No matter how highly you regard the series, most fans agree that the intro and the music that goes with it was the best and most memorable thing about the show. Judge for yourself.
Jessie. She had plenty of fans, obviously, such as those who saw her as a kick-ass female character and those who saw her as hot and those who liked her romance with Hadji or Jonny. Others, however, balked at the introduction of a new character to the mix, while others saw her as a Faux Action Girl (her Badass Decay in season two didn't help).
It also didn't help that in the very first episode, "Darkest Fathoms", she ends up as a Damsel in Distress, which became the impression many early reviews of the show got of the character, not giving the show a chance to show her badass moments later on in the season.
James Compton, from "AMOK", is a former special forces operative thought killed-in-action but now working as a freelance mercenary for whoever can hire him. Paid by a private party to investigate a hindrance to the drug trade in Borneo, Compton assumes the identity of "Mitchell Stramm" after his party is seemingly wiped out by the native Amok monster, winning his way into the Quest's family's good graces and finding the village that's been disrupting the drug trade. Smugly betraying the Quests at this point, Compton opts to simply massacre every last native man, woman, and child in the village to remove them as an obstacle, gloating that his employers will pay him handsomely for each head he brings back to them, attached to the bodies or not.
The succubus/vampire known as Elise Lenoir, from "Eclipse", initially appears to be a victim, an innocent young woman on the run from evil men. The twist comes when it's revealed Elise was maintaining her youth and beauty by draining the life from beautiful, innocent women, and the man hunting her was trying to avenge his sister when she fell victim to her. Elise murdered the men who tried to tail her, and later mind-controlled Hadji into her slave to bring Jessie to her for her food source. When her right-hand man protested about Elise trying to replace him with Hadji, Elise declared he was right and sucked the life from him as well. When her deadline of an eclipse was approaching, Elise abandoned all pretense of charm and subtlety and assumed her monstrous true form to kill everyone around and drain Jessie's life.
Dja'Lang Mukharno, from "Diamonds and Jade", is a puppeteer and brother of Kumar who exploits his people's old traditions for personal benefit. Coaxing his weak-willed brother into routinely selling off a rare gem to greedy buyers, Dja'Lang summons a shadow demon to brutally kill the buyers and anyone else in the premises to keep the money and the gem. Dja'Lang attempts to kill the Quest family and their friend Jade alongside the cops in the area when Jade sets Kumar up, and when Kumar loses the gem to the Quest family, Dja'Lang turns the shadow beast on him with full intent to murder him for his failure, laughing that he should have killed him years ago.
Critical Research Failure: "In the Wake of the Mary Celeste" has a man claim to be the reincarnation of the ill-fated ship's Captain Briggs. Doctor Quest, using information the man gave him, finds the wreckage of said ship. However, the Mary Celeste did not sink under Briggs' command, but was instead found adrift nine days after the last log entry. The actual Mary Celeste was deliberately destroyed thirteen years after the famous disappearance as part of an insurance fraud scheme, and its wreckage would have been off the coast of Haiti, not the Sargasso Sea as claimed in the episode.
Ethnic Scrappy: The first season's writers actually worked to avert this trope with Hadji, only for him to fall back into it in the second season with the reintroduction of the Sim Sim Salabim elements of his character. However, the first season's success at aversion is still debatable, considering they ended up turning him into a Bollywood Nerd computer expert (although that hadn't yet become a stereotype at the time the show was airing).
Though, to give the writers more credit, India was already headed that way in the 1990s, so showing Hadji as a computer-skilled youth was meant as a deliberately progressive portrayal.
Jonny's voice actor Quinton Flynn would go on to voice Raiden in the Metal Gear series, and mentions in this interview that he was told by the voice director (who also worked on both series) to imagine Raiden as an older Jonny Quest. Considering all the Narmandotherthings involving Raiden in that game alone (not to mention laterones), a lot of scenes from the show (plus the implications for poor Jonny) become beyond hilarious in this context.
Season Two's voice actress for Jessie was Jennifer Hale. Unfortunately, that was the season where the character had serious Badass Decay, but just look at that red hair and the flashes of Good Is Not Nice without picturing a teenage Jane Shepherd.
Memetic Mutation: "(Insert action here)... so it is written IN THE BOOK OF RAGE!!!"
Shipping: Compared to the previous versions of Jonny Quest, this version heats things up a little more than usual.
There is debate among who deserves to be the Fan-Preferred Couple. Jonny and Jessie for an part of the fandom, so like Hadji and Jessie are also well-liked,and the second season, Jessie was interested for Hadji, probably due to massive amounts of Ship Tease for both ships.
Apparently the series creators felt that Jessie would be the sort of girl Jonny would fall for when he got to the age where he'd be interested in dating, but the boss of the second season was more interested in Jessie and Hadji.
Even in the second season Jessie start to show more interest in Hadji, and even fall a crush for him.
Sent up in an episode where Jessie and Jonny had their bodies inhabited by a pair of star-crossed ghosts. They use them to reunite and depart for the afterlife, but not before engaging in a seriously intense kiss that Hadji eventually has to clear his throat to get Jessie and Jonny's attention to break up once they're gone. After some amusing awkwardness, Jonny checks some recording equipment they had set up to investigate the haunting, only to find that only a few minutes of footage had been recorded to account for over an hour of time. Jessie teases him with a drawling, "Yeah. The earth stood still for me, too, Jonny."
For a while, it was actually possible to get Word of God, at least for the second season. The short version was that they chose to split the difference between those who shipped Jessie with Jonny and those who shipped her with Hadji.note You can tell which writer shipped which from the ship tease. The shipping wars within the fandom managed to drive some fans into taking a third option: Jessie with neither of them.
Besides all that to say that some episodes still contained some decent Ho Yay would be remiss.
Sickeningly Sweet: In "In the Darkness of the Moon", Marie Metier calls Race "mon petit chou," which roughly means "my little sweetie" or "my little cupcake." Yes, Race.
The fact that Johnny's worst nightmare is being considered a failure and a disappointment to his father. And this isn't because of Johnny's mistakes either; apparently, deep down, Johnny wonders if his father thinks he's stupid. Poor kid...