Anvilicious: Every episode was designed to teach an important lesson via the human character Willy DuWitt. That this required a rather complicated plan on the part of the toads, and typically left them with a rather humiliating defeat, really hammered it home.
Designated Love Interests: It was implied a couple of times that Bucky and Jenny had feelings for each other (Jenny acting jealous when Mimi kissed Bucky and Bucky saying he'd trust Jenny with his life and would go to the ends of the Aniverse for her) but aside from these two instances, the two never showed any real romantic feelings for each other, although that could be explained by several factors: the war, their personalities (or lack thereof) and the brevity of the series.
Family-Unfriendly Aesop - Everyone in the Aniverse is fully aware that KOMPLEX is the only reason the Toads act as they do, yet they have no qualms with causing as much damage to them as possible or insulting them in some pretty harsh ways.
It may be because even before KOMPLEX the Toads weren't exactly the Aniverse's greatest bunch of guys to begin with. They were a society so decadent and lazy that they desiged an AI computer system to take care of even the most mundane tasks for them.
Still, the backstory provided still emphatically explains how they kept to themselves and didn't hurt anyone and had families and a society pretty much identical to the mammals' (aside from their diets). Decadent and lazy, yes, but mostly good. Their only "crime" pre-Komplex was lack of foresight.
Heartwarming Moments: After rebuffing a pretty young classmate who was trying to get him to help her cheat, finally realizing he can't let himself be fooled into thinking she likes him, Willy's girl pal gives him a kiss for wising up.
Nightmare Fuel: The Matter-Transmuter. It doesn't work on living matter, true, but what happens to the people on the planet that was just turned into a cupcake?
Actually, it was a ship that got turned into a cupcake, and the crew could be seen floating away safely in space with parachutes—which, while it presents another physics problem, is par for the course for this series. Plus that was just on a propaganda video for KOMPLEX anyway, with scenes that probably weren't really happening. The planet that got transmuted was Toxus 2, which Willy mentioned was uninhabited before transmuting it into a giant Berserker Baboon to scare the toads away. Again, weird physics: apparently the gun can turn a barren planet into a living organism, just not affect living things directy. The real Nightmare Fuel is that the gun overloaded and blew up after that... meaning that there is a planet sized baboon that can apparently breath in space still wandering the Aniverse...
The Scrappy: Willy, for people who thought that the show would've done fine without him.
No Problem with Licensed Games: The tie-in NES game was popular among many of those who played it. The arcade game, which allows Bucky to defeat the toads once and for all, is without a doubt awesome.