The titular team defeating Blowhole's entire army themselves.
How about Kowalski defeating multiple enemies blindfolded in "The Hidden?" This moment also coincides with him finally learning to trust his gut instead of always scientifically analyzing everything to death, even getting praise from Skipper for finally trusting his gut. Too bad the chameleons turned out to be friendly chameleons...
Private in "Untouchable." When a Jerk Ass poison dart frog terrorizes the whole zoo by getting everyone to cater to his whims (with a threat of poison if they disobey), it's up to the usually meek Private to set the frog straight. How does he do this? By building a robot suit to hug him... and then threatening to pop him like a grape if he disobeys.
Rico and feral Marlene's (brief) fight in "Otter Gone Wild".
Followed by Skipper's King Kong (1933) inspired dog fight with a toy plane before saving her and Julian from falling to their deaths.
Kowalski's epic banjo song from "Concrete Jungle Survival."
Skipper escaping from the gut of a giant carnivorous fish near the end of "Snakehead".
Eggy (the duckling the penguins raised as an egg in one episode) proves to be a superior combatant than the penguins due to him learning all of their skills. So, how is he finally defeated? By King Julien dancing. Yes, dancing. Eggy can't lay a finger, erm, wing on him.
Private's mini-golf game vs. the armadillo in "Mr. Tux". Private wins... with the help of a cricket.
Private freeing the lemurs from the "Graveyard Eight" bus.
No mention for Hot Ice yet? SHAME!ON!YOU! The penguins GOT 2 ROBBERS ARRESTED IN A HEIST!
King Julien gets another one in The Lost Treasure of the Golden Squirrel. After all of his friends succumb to their greed after gazing into the mystic key's eyes, Julien decides to take a look at his depraved desires. However, he is surprised to see that his vision shows him what he already has: loyal servants, a vast kingdom and a throne. He then goes to realize that he is the one who is the purest of heart, and to survive the cursed room of treasure, they must throw all the treasure to the rats! With no treasure on their side they are light enough to rise to the surface. King Julien. Saved his friends. From drowning in lava.
Everyone was more than surprised about this.
Private beating up the Red Squirrel with his Lunacorn doll,and defeating him by activating its glow function, which sets off the Squirrel's light sensitivity.
"You're just jealous I have a Lunacorn and you don't!"
An amnesiac Skipper describing snowcones to Alex the Lion while beating up a shark! Yeah, awesome.
The musical numbers in "Blowhole Strikes Back" are all pretty awesome in their own right, particularly both of Blowhole's numbers and Julien's number.
Kowalski single-handedly saving the Earth from being blown up by Martian space squids via an army of Jiggli.
"Cute-astrophe" culminates in Private finally standing up to Skipper and the others, flat-out refusing to use his weaponised cuteness factor anymore. Even when it looks like he'll have to use it to avoid the team being shipped off to Denmark, he sticks by his guns and ends up fighting off all three of the others at once. Badass Adorable at its most adorable.
After Julian finds out that the baby Fusa (a species that usually eats lemurs) thinks he's it's daddy, he promptly goes Papa Wolf to save it from a giant snake. Including telling the Fusa to bite his tail so it can hang on while he runs on all fours and telling the snake to eat him first when they get cornered (Julian hopes his fluffy nature will choke the snake, making it unable to eat the baby).
And the the Fusa cub beating up the snake when it tries to eat Julian.
After being busted by the penguins, the Archer continuously attempts to distract the penguins to make his escape. Skipper however doesn't budge and corners him, while Private gives him a thorough telling off.
Episode 15, "Litle Zoo Cup": The penguins are pimping the car while "Wheels of Thunder" plays in the background.