Angst? What Angst?: Throughout the series, but most apparent in The Movie, when Eliza disappears from boarding school on another continent, and no one expresses any emotion other than annoyance at the fact that a child is missing.
Broken Base: Not just among Nickleodeon fans (most of which think this show is the reason why Nickelodeon's programming has gone downhill), but among professional zoologists. Some believe it is overly anthropomorphic and encourages dangerous attitudes towards animals, whilst others think that the anthropomorphism and breaks from reality are justified in order to get children interested about zoology.
Designated Villain: The customs agent in "Chew if By Sea." Admittedly, he's a Jerkass who keeps animals in uncomfortable conditions so it's hard to like him. But the show treats him doing his job (preventing the smuggling of exotic animals) as villainous, in and of itself, as if he's to blame for Eliza bringing Emily the wombat into the country.
Jerkass Woobie: The stoat from "Show Me The Bunny". Sure, it's out to kill the titular bunny (which isn't a villainous act given it's just a predator) but at some point, it gets captured and almost killed by poachers. After Eliza rescues it, it goes right back to chasing the bunny.
Just Here for Godzilla: Many people who have watched the show like to admit that they found the aforementioned Nigel Thornberry to be the best part of the show and wish that he had been the main character instead of the base-breaking Eliza.
Hollywood Homely: Eliza is actually really cute for a pig tailed, glasses wearing nerd. Especially in the later seasons where she lets her hair down and stops wearing the violent yellow skirt and T-shirt hybrid she usually favors
Granted, according to the book Not Just Cartoons: Nicktoons, this was more a case of Executive Meddling.
On the other hand, the creators were hellbent on ensuring that Eliza never, EVER had her braces removed, as they wanted it to be a more benign detail about herself in order to make children with braces feel less self-conscious.
Lost in Medias Res: Because there was no "origin" episode, viewers were expected to simply assume that, for some reason, Eliza can talk to animals because of a Shaman and that they had a feral child named Donnie for no apparent reason. While the shaman was at least shown in the introduction, how they found Donnie wasn't explained until a Made-for-TV Movie. Although there was an origin episode in the second season "The Gift of Gab" which was a Whole Episode Flashback, and the opening sequence does show how Eliza gained the power to talk to animals.
And a more recent one, also concerning a Nigel Thornberry: combining his unintelligible gibberish from a random episode with a well-known song and then photoshopping his face onto the single/album cover. Blaaaaaarghghghgh.
This tendency has now extended to photoshopping his face onto gifs of scenes from Disney movies; later, this extended to any cartoon character and then even further, to anything that can be readily photoshopped (especially gifs where characters appear normally at first, turn away or hide their face temporarily, and return with Nigel's face). They often vary between Uncanny Valley to outright Nightmare Fuel. Example.SMASHING!◊
Moral Event Horizon: In The Movie, Sloan and Bree's plan to kill a thousand elephants...simply so that they can get the ivory. Later, they threaten to murder Debbie to get information out of Eliza (Bree implies that she actually wants to kill Debbie instead of simply getting information.) And if that isn't enough, Sloan later tosses poor Eliza into a raging river for interfering with his plan.
If there's one thing most people remember about this series from their childhood, it's the "Naimina Enkijio" episode, mostly for being Nightmare Fuel incarnate for many kids of the 90s. The fact that it's based off an actual legend doesn't help. Such examples from that episode include; creepy wailing from a Ghost Girl constantly calling Eliza's name, Eliza seeing the Ghost Girl as her reflection in a swamp that supposedly grabs and drowns children, and the general creepy atmosphere of said episode thanks to taking place in dense, dark forest.
Nowadays, the show is best remembered for Nigel's "Blaaaaargh" moment and his "Smashing" face.
Tyler, Eliza's annoying and haughty cousin, who becomes a main character for part of season 3.
Shane also counts. Not only is he a completely unnecessary Satellite Love Interest for Eliza, but the audience is also supposed to like and agree with him despite the fact that he endangered not only himself, but Donnie and Eliza as well, a toddler and a preteen, respectively, and see him as being in the right when his only concern afterward was insulting Eliza, who was understandably furious at his incredibly reckless actions. And that's just his first episode.
Seasonal Rot: From season 3 onward. The show starts focusing less on the animals and locales, and more about high jinks that just happen to involve talking to animals and may or may not feature Idiot Ball play. For comparison, season 2's "Chimp Off the Old Block" centers on the social structure of chimpanzees, and the show's finale "Eliza Unplugged" in season 5 centers on Eliza struggling to confess her love to a pop star.
Some Anvils Need to Be Dropped: While the show didn't break any ground by pointing out that poaching and the exploitation of animals is terrible, it did occasionally argue that misguided attempts to "help" animals who are apparently suffering often makes things worse.
Case in point: when the Thornberrys are on the Galapagos islands, Eliza stumbles across a finch attempting to spear some hidden insect larvae with a thorn. She decides to make his life easier by giving him (and later on, additional finches) sewing needles. The finches quickly devour the insect population and soon the entire food chain has fallen apart.
Another episode had Eliza trying to free an elephant calf from a nature preserve, both of them believing the place was a prison...until she succeeded, saw just what poachers can do to wild elephants, and found that the calf's mother was deeply relieved to discover her behind that gate.
All in all, the moral of the show seems to be "The animal kingdom is beautiful and worth protection, but that doesn't mean we get to impose what we think is right on it." It's the rare Green Aesop that shows the need for intelligent, thoughtful conservation efforts rather than blind attempts to "fix" what's wrong without knowing the whole story.
As mentioned above, the show exposing the atrocities of poaching being nothing new, they did an excellent job of showing just how far poachers will go to get what they want in several instances, poachers had no second thoughts about attempting to, or in the case of Donnie's parents, succeeding in killing humans to get what they want.
Squick: In "The Origin of Donnie: Part 2", Eliza chews some fruit for a baby orangutan. Lampshaded by Darwin.
Uncanny Valley: Baby Donnie's proportions are... off. Likewise for a solid portion of the characters — it is Klasky-Csupo after all.
Wheelchair Woobie: A character of the week was one. The conflict came from Eliza trying very hard not to seem like she's pitying her just because she's in a wheelchair, eventually annoying her.
The Woobie: Quite a few one-shot animals characters actually. Like the hyena from "No Laughing Matter", Emily the wombat from "Chew if By Sea", the rabbit from "Show Me The Bunny" or Tano the cheetah cub from "Cheetahs Never Prosper".