In chapter 3, Luz compares the Deadly Game she's in to Danganronpa noting she's played and watched far too much of it to know how that would end in this scenario.
Marcone Giovanni's Quirk "Life Giver" which is basically the life giving ability that Giorno's Gold Experience from JoJo's Bizarre Adventure: Golden Wind has, aka turning inanimate objects into living beings that served the user. Hell, they have similar last names and have an Italian theme.
In Chapter 8, Hilbert admits to Stanley he named his Quirk "Cleave" after Sukuna's Cursed Technique
Sophia Humbolt's "Limitless" Quirk is a reference to Gojo Satoru being a partial but still powerful version of it with "Red" and "Blue". After steals and evolves the Quirk, she can create Hollow Purple.
In chapter 4, Judy's Portable Hole Quirk is the basically the same power as the villain Spot from the Spider-Man comics, as Stanley lampshades when witnessing it in action.
In chapter 11, Luz mentioned using Julia's Quirk "Vines" to swing through the trees like Spider-Man swings around. She later gives it to a boy that wanted to emulate said hero.
In chapter 15, a girl in Texas was described as having the same powers as Magneto and behaved much like a typical supervillain.
Carla Tsunata's Quirk "Black Cat", was basically a homage to the Zoan-type Devil Fruit from One Piece. Think Rob Lucci's Fruit but a black cat instead of a leopard.
Cody Johnson's Quirk "Flame" is based on Portgas D. Ace's Flame-Flame Devil Fruit allowing him to create, control and transform into fire.
In chapter 17, All For One is surprised to hear Luz has read One Piece as well. Although he mentions its called Two Piece in his world.
Hunter's "Lightbringer" Quirk is very similar to Glint-Glint Fruit, which allows him to manipulate, create, and turn into the element of light. Luz even refers to him as a Kizaru knock-off.
Others
In the rewrite of Chapter 3, when Luz was talking with Kennedy and he asked what was her favorite band, she mentions her favorite one is NateWantsToBattle, with her favorite music from him being "The Finale", A Five Nights at Freddy's fan-song. Further on, it is revealed Kennedy is a huge fan of Puella Magi Madoka Magica and Naruto.
In chapter 4, Luz mentally comments in the Death Camp predicament she probably looks like a frightened dog whimpering as they were chained up to be shot in the face point blank with a shotgun. The girl then notes play way too much Wolfenstein if that was the first thing she thought of.
Luz recalls a time when she was little when she worse a Shrek T-shirt and regretted it ever since.
In chapter 6, Luz mentions to her team that she's played a handful of strategy games to some form of game plan, including Command & Conquer. Some of her team members, like Marcone even refer to her as Commander, and Carla mentions her mom used to play that game.
Luz learned from Death Note that a white lie can contain a nugget of truth to deceive the person being lied to. She also mentions she loves binge watching The Legend of Korra.
In chapter 7, Luz compares All For One squatting in her Mental World to like a A Nightmare on Elm Street situation, just without the threat of dying.
Julia once bought copies the of first books of The Dresden Files but unfortunately her fundamentalist father quickly burned them once he discovered them.
In chapter 10, Luz notes she's seen in anime like Death Note, and Dragon Ball, where the main character would have so much confidence in their abilities that they’re able to take down any threat before them, even if said threat is vastly superior and stronger than them.
The Spear Fingers Quirk originally from Darlene sound a lot like the main power of Lust the Homunculus from Fullmetal Alchemist.
