A usage wick check found that what I suspected was true, and that most usage fell under "work features a penguin" or penguins being mentioned. None of the wicks I checked mentioned ratings or popularity due to penguin inclusion. I also saw a small trend of potholing the trope to the word "penguin", regardless of the situation, but not enough to show that the trope is a Pothole Magnet. The breakdown is as follows:

• Work features/mentions penguins: 24/52 | 46.1%
• ZCE: 10/52 | 19%
• Penguin-themed object: 6/52 | 11.5%
• Character dresses up as a penguin: 5/52 | 9.6%
• Unsure/Other: 5/52 | 9.6%
• Cute Penguin, Funny Penguins, and Penguins as a main character each had 1/52 wicks | 1.9%

Originally, I was looking to see if anything could be split off and sent to TLP, but with over 50% of the wicks being misuse in some way (including one wick that was potholed to "Everything Better With Flamingos"), I think a more likely action would be disambiguating this between several other tropes much like what was done with Everythings Better With Dinosaurs and Everythings Better With Plushies.

Some disambig targets:

• Cartoon Penguin: Stock cartoon portrayal of a penguin being black and white with no species-specific details.
• Penguins Are Ducks: Penguins given duck attributes due to unfamiliarity with penguins.
• Polar Bears and Penguins: Penguins and polar bears co-existing in a work even though they don't in real life.
• Polar Penguins: Penguins used as a visual shorthand for cold climates.
• Flying Flightless Bird: Penguins are able to fly in the work.

• The Corpse Stops Here: The first Paper Mario, where he stumbles on a dead penguin and the penguin police arrive moments after. He wasn't really dead.
• Animation.The Minds Eye: "The Ascent Of Man" has a few of these. One transitions from a waterfall to an Antarctic landscape (featuring a penguin) with the latter shot's camera peeking out from behind a rock. Another transitions from the exterior of a Mesoamerican temple to the interior of an Egyptian temple. This is accomplished when a painted pillar wipes the screen to the left and brings another scene with it.
• Anime.Hakushon Daimao: In one episode, the main characters help a homesick penguin.
• AvatarTheLastAirbender.Tropes A To H: Incidentally, they're also otters.
• Blog.Huxley Paleozoo: Giant prehistoric penguins!
• Blog.Things Mr Welch Is No Longer Allowed To Do In An RPG: 635. Arguments cannot end with the statement "Alright, we'll settle this like penguins!"
• Characters.Battle Spirits Saikyo Ginga Ultimate Zero: [Laila] She's a huge Pentan lover.
• Characters.Rainbow Magic: [Pia] Her job is to protect the penguins.
• Characters.Samurai Flamenco: [Moe] Her favorite animal along with rabbits, as stated in the first Character Talk CD. When she has to create an Imagine Spot date, it's just about penguins.
• Characters.Vocaloid: [Big Al] A minor meme at most, but he seems to have a good relationship with antarctic animals.
• ComicBook.Pink Chickens: A page in episode 13 has "the characters you've come to know and tolerate" drawn as penguins "due to stuff".
• ComicStrip.Mutts: One storyline has a penguin, bored of Antarctica, fly to where Earl and Mooch live. No, really. He flies there.
  Mooch: But I don't believe penguins can fly!
  Penguin: I know. But I do.
• ComicStrip.Shermans Lagoon: When Sherman and Ernest go to the South Pole, they encounter penguins. One of them attempts to fly... and ends up injuring himself.
• ComicStrip.The Far Side: Used occasionally, but no more so than any other animal.
• DarthWiki.Charms Dealer: Slick Petey from CD3.
• Fanfic.The Games Of The Gods: The gag for chapter 8 "Mush" has a gratuitous "Canadian penguin". It talks.
• Film.Mary Poppins: The penguin waiters in the animated sequence.
• Film.Stage Struck 1936: George takes Ruth to the aquarium. They go to see the penguin exhibit, and George suggests that he looks like a penguin when he puts on formal wear.
• HIMYM.Tropes Season Five: One of the ways to defuse a pissed-off Robin is to talk about emperor penguins.
• LetsPlay.Flux Buddies: Nano has a pet penguin named Billy that she keeps around the base. Unlike Tiddles, Billy gets resurrected and eventually survives after Kim and Lalna leave the Flux Buddies 2 base.
• Literature.The X Ray Picture Book Of Incredible Creatures: The Emperor Penguin is featured along with its x-ray.
• Music.Songdrops: Two songs are "Poopers the Magic Penguin" and "Ten Little Penguins".
• Series.Impractical Jokers: Murr once played a zoo worker who quits because he's tired of all the "penguin drama." He fails to get anyone to sympathize with him.
• VideoGame.Redemption Cemetery: The penguin exhibit shown in the zoo-keeper's memories in Salvation of the Lost. A sign reveals that they're pretty aggressive.

• Characters.Blinky Bill: [Flap] He dresses up as one in the third season during the trip to Antarctica.
• Characters.Cookie Run S Rank Cookies: [Peppermint] Peppermint Cookie has a Baby Penguin Costume.◊
• Characters.Dance Dance Revolution: [Ronpei] Dresses up as a penguin in Supernova 2 to enhance the cuteness of course.
• Characters.The Crumpets: [Larry] In "The Clip", the gang have him wear a penguin costume for their viral video production. The unintentionally-produced final video depicts him singing and hopping on a toilet with an elephant sitting on another toilet near him and stomping the floor.
• Podcast.Wreckless Media Radio: Brandon once walked into the studio unannounced, wearing a penguin costume.

• I Shall Taunt You: [Doctor Who] Expanded Universe: The Doctor does this a lot, but in the Eighth Doctor Adventures novel Camera Obscura, he goes all out in one scene, mostly just to get back at Sabbath for making his life very, very difficult. He does all kinds of intentionally romantic things (well, Sabbath did steal his heart), hides a whoopee cushion in his sofa, flops on his desk like a cat while Sabbath is looking at something, folds his papers up into penguins, sings to him, etc. Do not piss off the Doctor, or he'll teach you how it's done.
• Characters.Game Grumps Team Grump: [Barry Kramer] Apparently has a penguin calender, where he himself places a speech bubble reading "SQUARK!" on every one.
• Characters.Gundam Build Divers: [Momoka] Her Momokapool is a Kapool redesigned to resemble a penguin.
• Characters.Happy Tree Friends Main Characters: [Flippy] [RealMenWearPink]: Besides collecting weapons in his bunker-house, he likes flowers, tea parties, pink penguins, and unicorns/alicorns. According to the "Collect Them All" section (From the "First Blood" DVD), Flippy also knits sweaters.
• Literature.Anita Blake: Anita's favorite—and comfort—stuffed animal is a penguin, and her "comfort shirt" has penguins on it.
• Literature.Misery: No, seriously. Annie owns a little model of a penguin on a pedestal. It becomes surprisingly memorable. Five words: "NOW MY TALE IS TOLD!"

• LightNovel.Heavy Object: The sight of a group of baby penguins walking through the snow is enough to make both sides of a battle stop firing at each other and just Squee over the cuteness.

• Anime.Penguindrum: Penguins 1, 2 and 3 are a major source of the Plucky Comic Relief, and penguins and penguin iconography are pervasive throughout the series. May also qualify as main characters.

• Literature.Tacky The Penguin: The heroes of the series are a small group of penguins.

• Anime.Battle Spirits Heroes: Pentans, more rather.
• Anime.Makai Senki Disgaea: As usual, dood!
• Characters.Amagami: [Sae] Her arc's epilogue.
• Characters.Dragon Fable Party Members: [King Linus] Just the trope name.
• Characters.End Roll: [Pengi] Just the trope name.
• Characters.Sweets Fairy: [Tiramisu] Just the trope name.
• Characters.You Are Being Summoned Azazel: [Yuichi] Just the trope name.
• Manga.Tuxedo Gin: Just the trope name.
• Roleplay.Personification Life: Just the trope name.
• Series.Pythagora Switch: Just the trope name.

• Do Wrong, Right: In the German comic Ingo Pien about humanized penguins, a Neo-nazi sieg-heils in court. The judge reprimands him: "If you ever do the 'sieg-heil' again... do it smartly!"
• BetterThanItSounds.Video Games D To F: Disgaea: Hour of Darkness Demon prince oversleeps, must reclaim kingdom with dead criminals.
• Creator.Benedict Cumberbatch: He is also famously incapable of pronouncing the word "penguins".
• Creator.Nao Touyama: [AnimalLover] She is very fond of Penguin and owns an annual pass to the aquarium so she can see them whenever she wants. She even uses penguins as mascot in some of her works or some case her characters become relate with them too.
• VideoGame.Need For Speed Heat: Neon flamingos are everywhere around Palm City. They're collectibles you can drive through, which gets lampshaded by the player while talking to Lucas about this trope. Yes, this was potholed to "Everything's Better With Flamingos".