These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Alternate Aesop Interpretation: There's the Green Aesop about overfishing, pollution, global warming and animals in captivity. And then there's the Aesop about being yourself. And then there's the Aesop that you should not put all your faith in religion but also need to take action yourself. And then there's the Acceptance Aesop, where you're encouraged to accept others for who they are. While many Acceptance Aesops in children's films recently have been the Gay Aesop (and that is still some people's interpretation), Happy Feet seems more about accepting people on the Autistic Spectrum.
Alternate Character Interpretation: Perhaps the whales were just trying to get the plastic holder off of Lovelace's neck the whole time, then chased them onto shore and left? Would explain why they focus on him in particular when the others are perfectly fine meals in and of themselves.
Anvilicious: the "save the penguins" message is too heavy-handed.
Several, but basically anything The Amigos and Loveless say.
The conclusion of the chase scene of Mumble and the leopard seal. "Oh no, he's coming! We'd better move in half an hour!" And then slow-mo running. Yeah.
When Mumble first displays his awful singing to the Amigos. "Yeah, I knew an animal who made that noise once. But then we turned him over and he was dead."
When baby Mumble asks about the GPS tracker on the lead skua's ankle, the skua (which for some reason has a Boston accent), launches into a story about how he was "abducted by aliens" (tagged by researchers and released). The others in his band kvetch about it to no end, and it's strongly implied that they've heard this story many times— to the point where they're mouthing along with his spiel behind his back.
Gloria's rendition of "Somebody to Love" and "Boogie Wonderland" deserve mention. Then again, all the music in the film had the same unique sound and great energy to it. The actual score - as opposed to the songs - has some particularly breathtaking moments.
The sequel has the ultimate rendition of Queen's "Under Pressure," for its climax!
Come on, admit it: You got chills when you heard Erik singing the bassline.
Mumble's birth. All the other chicks are running around with their fathers, all the eggs have hatched, and his egg...is just silent. Maurice's weak assurances ("It happens sometimes"), coupled with Memphis's guilt-ridden, heartbroken expression is just...ow.
Uncanny Valley: During some of the more obvious motion capture sequences, as you may have noticed that human anatomy and penguin anatomy is wildly different. Plus there's something unsettling about seeing Elijah Wood's eyes looking out of an otherwise realistic penguin face.
The choice of director is the most baffling thing about the entire film. A movie about dancing CG penguins... directed by the same guy who directed Mad Max.
Not as shocking when you consider that this and The Road Warrior are basically the same film - except that one involves penguins and is generally less bloody, and the car chases are substituted with musical sequences.