The scene where Rai finds out Lelouch is Zero is nearly identical to where Ned finds out Peter is Spider-Man in Spider-Man: Homecoming.
Before they learn that the official term for it is Geass, Bumblebee dubs it "the Stare".
When Soundwave finishes his online search for info about the Black Knights in Chapter 7, We get this little nod to Superman vs. the Elite:
Thundercracker: Over 3 million hits online on Prime and Zero. [turns to Soundwave] How many of them are informational? Soundwave: [Displays the number 0 on his face plate] Skywarp: [Smirking] How many of them contain the phrase: "These guys are awesome!"? Soundwave: [one million, two hundred and three thousand, four hundred and seven]
When C.C. explains to the Autobots about V.V. in Chapter 20, Cliffjumper asks if there was an A.A., B.B., R.R., D.D. ...Note that C.C. and V.V. are pronounced 'C-2' and 'V-2' respectively.
Chapter 22 has Airachnid questioning Cornelia regarding the reasons Euphie remains alive despite Britannia's motto regarding social Darwinism. In the author's previous fanfic, Fairy May Cry, Vergil questions Ultear about why Gray still lives despite her existing resources and motives to kill him; these are the same circumstances the Decepticon questioned Cornelia under which gets into her nerves.
In Chapter 27, Ironhide saying that Suzaku needs to drop his Never My Fault attitude if he were to join the Black Knights and Autobots is very similar to the moment in One Piece where Zoro states Usopp needs to apologize before rejoining the crew. He even states that if Suzaku doesn't comply but still gets to join, he'll leave; something Zoro says as well.
Chapter 31 has Luciano Bradley (upon first meeting Starscream and Dreadwing) ask casually, 'does their kind bleed?'
Chapter 32 has Skywarp briefly refer to Luciano Bradley as that “Vampire Knight guy" when suggesting the possibility of the latter fitting into the Decepticon ranks. For bonus points, Luciano’s English VA voiced Zero Kiryu in said series.
Chapter 33:
In the beginning, when Cornelia confronts the Vehicons, she invokes a certain God of Thunder by yelling "BRING ME MEGATRON!".
When Cornelia confronts Megatron over Euphie's kidnapping, her wording takes cues from Kingpin in Daredevil (2015).
Cornelia: I am going to kill you! Megatron: (readies his blade) Take your shot.
Chapter 34:
There's quite a Freeze-Frame Bonus if one reads the reaction of the royals to the beginning of the Decepticon attack. The royals' reaction describes them as "like watching people turn into cows", followed by a statement that it's alien to them. Put two and two together, and you have a sly reference to Animorphs, to which Hasbro also managed its toyline under the Transformers license.
Charles' reaction to the Decepticon attack on Pendragon is to break the Stunned Silence by shouting "Are we blind?" and ordering a counterattack, just like Director Krennic does in response to the rebel attack on Scarif in Rogue One.
After their battle and him putting his former disciple under the power of his Dark Geass, Megatron's "The Reason You Suck" Speech to Charles, as well as their positions, is very similar to when Alucard confronts Walter.
Upon the successful attack on Pendragon, the Nemesis blasts out the Royal Palace that resembles the trademark scene of Independence Day where the aliens blast the White House in a fiery explosion.
Chapter 35:
Shirley manages to save her Autobot comrades by tossing an outdated model into an Insecticon and launching it into space. Specifically, she utters, "GET AWAY FROM THEM, YOU MONSTER!" If she can swear, she'd make Ellen Ripley proud.
Chapter 36: Ohgi's Rousing Speech to the rest of the Black Knights in light of the Decepticon victory is at least slightly based on Dillon's from Alien3.
Johann Schwarzer's death is much like Sir Penwood's.
Slipstream uses Titan's line about the Area 18 rebels not being free so much as "under new management" before turning on them.
A world where a war between otherworldly beings in robotic form fighting out in the real world and forcing the world's nations to pick a side? That screams Aura Battler Dunbine.
The cybernetic leg braces that allow Nunnally to walk again are based on the ones used by War Machine in the Marvel Cinematic Universe.
The Dark Knight Headmasters' Knightmares are loosely based on the main Gundams from Mobile Suit Gundam Wing, in particular, the Endless Waltz OVA.
The name of the Dark Queen's Knightmare, the Dark Excalibur, can surely raise eyebrows among readers familiar with Fire Emblem.
This isn't the first time this plot beat of the main villains using the corpse of a protagonist's parental figure is employed in an Iron117Prime story either. In Fairy May Cry: Devil's Retribution, Sanctus and the Order of the Sword use Sparda's corpse to power the Savior, which didn't sit well with the protagonists.
In the same chapter as above, the family dynamic of the first Code Bearer and his children bears similarities to the Mortis family: an all-powerful father, a good daughter, an evil son that turns on his family.
Her boasting against the heroes before being silenced by a big "SHUT UP" remark seems to take after one of Iron117Prime's works, specifically Tangled With Ninjas. Simply replace Airachnid with Pythor and Kallen with Eugene.
Chapter 15:
Tamaki played a certain Led Zeppelin song during the battle. There's also how Warpath calls out to Starscream when Grimlock joins the fray, both of which bring to mind Thor: Ragnarok.
The High Eunuchs beg Grimlock not to kill them, with him replying "That pleasure belongs to someone else." before allowing Xingke to kill them. This is similar to the exchange between The Hulk and Red King in Planet Hulk.
Ashley makes a funny remark, and then gets chastised by Jean, to which he replies that they're in a tense situation. It's not too dissimilar to Worlds Collide (TMNT) where Sokka makes a quip while fighting the Shredder.
Chapter 26:
Lelouch channels his inner Aizawa when confronting V.V. over all of his heinous actions.
Lelouch: All the hundreds or even thousands of innocent people you and Charles hurt or even killed... Those you toyed with and those who cared for them... those that you never even gave a single thought for... do you know what they say...?! It's our turn to take something away from you!
V.V. channels his inner Goku Black when he is about to fight Lelouch and Optimus.
V.V.: This is it Lelouch, Optimus…! For your crimes against me and my brother… for your very sin of existing… for the sake of my vengeance… YOU WILL DIE TODAY!
When Megatron enters the battle. he makes a dramatic entrance as he crashes down onto the field and pulls his Dark Star Saber out while stating "Well don't stop on my account." with a grin. This is like what King Andrias from Amphibia did when he joined the fight against the resistance in "The Beginning of the End".
With both the heroes and villains squaring off against one another, only for a super weapon to break up the fighting, the setup is similar to Kingdom Come complete with the large body count between both forces. To add insult to injury, Megatron manages to survive much like Superman did, albeit with less damage.
One of Nunnally's thoughts for Marianne was probably her having a cloned body with her consciousness in it. This harkens towards Worlds Collide (TMNT) as this was the fate of Hama before she disintegrated during the final battle between the Shredder and the heroes.
Much like what Qrow did to Ozpin upon learning the full truth of Salem, Lelouch's reaction to learning of his mother's involvement with Ragnarök is to punch her across the face in a fit of rage. Also, similar to how Qrow said meeting Ozpin was the worst luck of his life, Jeremiah says that pledging his loyalty to Marianne was the worst mistake of his life.
Marianne getting punched by Lelouch in general is somewhat similar to Minato Namikaze getting punched by Naruto Uzumaki. Marianne's actions are what ultimately contribute to much of Lelouch's motivations to become Zero, much like what Minato did which later motivated Naruto to undergo his training. Not to mention that when their offspring first hear of their motivations, the first thing they do is land a punch towards their supposed parental figure. But while what Minato did was for the greater good, Marianne's actions are less noble and she makes it a point to atone.
For the record, this is the second time the author's pulled an Avengers Endgame homage; the first was in Frozen Turtles In Space, also in its final battle.
. Simply replace Airachnid with Pythor and Kallen with Eugene.