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.
Yakko and Wakko's rendition of "Copacabana", as it applies to logs #2 and #3. And then Mordecai's munactually sang it! Since "Labocabana", Yakko's mun has also done "The Ink City List Song" (somewhat in lieu of the tune of Voltaire's "The USS Make Shit Up" (this and other interpretations are much to the mun's amusement, who specifically didn't have a tune)), "Labocabana Drinking Song" (parody of "Another Irish Drinking Song"), "Smooth Vegetable" (parody of "Smooth Criminal"), "Duck Police" (to the tune of the DuckTales video game Moon Stage Theme), and simply "Ink City" (to the tune of "Hotel California").
Heloise's mun provided "Diego", a parody of Lady Gaga's "Alejandro", about Heloise's conflict with Dr. Chipotle Jr.
Also for Heloise she's penned "Scientist!", parody of Little Shop of Horrors's "Dentist!" This becomes a bit of Fridge Brilliant hilarity when you realize Heloise's mun also plays Audrey II, and that Orin Scrivello was also Audrey II's first victim in-canon.
Misery's mun managed to turn Log #3 and Log #12 into musical numbers, by giving Heloise her own Villain Song - "Hely Knows Best" - to the tune of Tangled's "Mother Knows Best". Yeah, it's all kinds of awesome. (And then it was sung by the mun of Heloise! And it remained awesome)
Her second Disney parody - Conquer The World - was a love duet between Dr. Chipotle Jr. and Heloise, to the tune of Aladdin's "A Whole New World". Somehow, despite it's disturbing and gruesome lyrics, it's still surprisingly romantic and ends pretty sadly.
Genaleah, the game's owner and mun of many characters, gave us an Ink City version of The Dave Matthews Band's "Funny The Way It Is".
Fan Nickname: Various character nicknames have been coined by the game, such as "Hely" for Heloise and "Chippy" for Dr. Chipotle Jr.
Foe Yay: Heloise and Lucius, in the crack community especially.
Harsher in Hindsight: Can be coupled with Fridge Horror as the characters learn more about the world they've been pulled into. Another rich source for this is when characters are Put on a Bus, such as Misery's mundane implying she suffered Death by Despair following Thrasher's departure or Fluttershy being injured during the World Split.
Hell Is That Noise: During the World Split event, many... unpleasant sounds are associated with the City tearing itself apart.