Audience-Alienating Premise: Even those who know better not to believe the Animation Age Ghetto can't help but find the show ridiculous, simply because of how flat-out bizarre it's premise is (then again this was inspired by anime so...). Despite this, there are those who pushed past it and formed quite a cult fandom around it.
Crowning Music of Awesome: The theme used at the very end of the first season finale. Variations also include the music at the end of "I, Chiro". Even more epically, the music used when we first see Antauri as the silver monkey (complete with lightning crashing behind him) and all variations on that theme.
When fans are referring to the Season 2 finale ("Antauri's Masters" and "I, Chiro") and the Season 3 opener ("The Savage Lands" two-parter) episodes as a whole, they tend to call it "The I, Chiro Saga".
Jerkass Woobie: Clone Mandarin. C'mon, the guy gets his arm CUT OFF (on camera, no less!), is eaten alive by a giant worm-shaped incarnate of pure evil, starves, becomes undead, and eventually goes absolutely batshit insane in said worm, is later TORTURED for information for the whereabouts of his dead master's skull (again, on camera), and is then forced to become a pet-slave, which for someone with his pride, is a Fate Worse Than Death.
Moral Event Horizon: Mandarin crossed the horizon pre-series when he forced Nova into a freezing training room in order to "train her to survive harsh conditions" while continually lowering the heat and laughing at her. He only stopped when her Unstoppable Rage kicked in and blew him into a wall. It seems even more reprehensible when you take into account the fact that he did this before his Face–Heel Turn, while he was still considered one of the good guys.
Also, bug eating comes up at least once every other season. It's even the key to saving the day in one episode.
Chiro spends a good portion of "Belly Of The Beast" exploring the Dark One Worm's insides. He does not enjoy himself.
"Invasion of the Vreen" not only had Gibson eating a bug to save the day, but also when one of the Vreen was sliced in half and we had a view of its... err... parts. Gibson had the right to feel sickened by the sight.
Paranoia Fuel: It is said that the Dark Ones implanted offspring in the cores of "countless" planets. Take a moment to think about the concept that the planet you live on could be housing an enormous evil monster bent on instigating a Zombie Apocalypse on every planet in the universe, and you would have absolutely no idea until it hatched.
Squick: The monkeys tastes seem to extend outside their species. Sprx-77 is by the far the worst offender with his egregious love for human women (he gets better, though). Otto is the same, though to a far, far lesser extent. And there was even one instance in which Nova fell in love with an anthropomorphic cat.