Batman's costume and Powered Armor are both inspired by similar suits from the comic book.
Lines of dialogue are taken directly from it as when Bruce says "The world only makes sense when you force it to,", "We've always been criminals", "It's time you learned what it means to be a man", and when he says "I believe you" when Knyazev promises to torch Martha Kent.
Likewise, certain scenes- like Martha Wayne's death and Batman breaking through a wall to take down a mook with a machine gun- are direct homages to the graphic novel.
Superman drifting in space lifelessly, after tanking a nuclear explosion, in a near skeletal state is lifted from the similar scene where he diverts a Russian nuke from hitting the US.
Batman has a grappling rifle in one scene, referencing him using similar equipment in issue 1.
Robin's costume in display, with "HA! HA! HA!" written in yellow paint over it.
The big fight resembles the one in Darwyn Cooke's DC: The New Frontier series. In that comic, Superman was pressured into fighting Batman when a government official threatened his mother's life. When Batman has Superman on the ground, he taunts him with the expression "motherless alien". This offends Superman due to his mother being the only reason he's even fighting Batman. The fight is then interrupted by Wonder Woman, who convinces the two that they need to take control of the situation. Also, Superman was seemingly killed by a greater threat.
Much like in The Dark Knight Strikes Again, Batman tries to brand Lex Luthor. But purposefully misses as he's gone through some character development.
A brief moment in the Comic Con trailer seems to reference the book, as seen here.
Superman is surrounded by a crowd who reach out their hands to touch him is a recreation of a page from Superman: Peace On Earth.
Just before leaving Lex's event to intervene in the botched Day of the Dead celebrations and save the young girl from being burned alive, when noticing the news broadcast, Clark's hand goes to his tie as he turns away, clearly intending to perform the iconic shirt rip.
From the "Knightmare":
The masked troops surrounding Superman bring up Regime Superman from Injustice: Gods Among Us, even donning a Superman emblem on their shoulders, and the villainous Superman rips out Batman's heart because he "took Lois from him". Injustice depicted a Superman who turned villainous because Lois Lane was murdered.
In the same sequence, Parademons appear fighting on Superman's side, evocative of Elseworlds' Superman: The Dark Side, in which Superman's rocket is diverted to Apokolips and he grows up as Darkseid's adopted son.
It is also an homage to the series finale of Superman: The Animated Series, in which Superman is brainwashed and forced to serve as an agent of Darkseid.
The Comic Con trailer features a shot of people standing on a roof with the "S" shield painted on it to signal Superman for help. The same method was used in Superman: The Man of Steel◊ #18.
In the "Lexical Analysis" interview, Luthor dismisses Batman's intimidation tactics as "cowardly and superstitious", recalling a recurring quote used by Batman in the comics, "Criminals are a cowardly and superstitious lot."
In the building where Batman nearly killed Superman, one of the graffiti on a large column is a distinct question mark.
Bruce asks Alfred that after 20 years in Gotham, "How many good guys are left? How many stayed that way?" He's most likely talking about Two-Face. While the former could refer to Jason Todd.
When Batman gasses Superman with powdered kryptonite, he tells him "That's fear you're breathing." He obviously borrowed that gimmick from Scarecrow.
Bruce sarcastically notes to Clark that Gotham has had "a bad history with freaks dressed like clowns."
When Bruce assaults the warehouse at the end, the combat sequence is similar to the "Arkham" series of games. In fact, the device he uses to render several mooks' guns inoperative is straight out of Batman: Arkham Knight.
Perry mentions that the Daily Planet was built around 1938, the same year when Action Comics #1 was published.
Speaking of Action Comics #1, the famous cover depicting Superman lifting a car can be seen recreated as a news photo in a Freeze-Frame Bonus moment (seen in Wallace Keefe's hate-shrine to Superman).
In one scene, Superman was counseled by the "ghost" of Jonathan Kent, similar to Smallville in season 10.
In Post-Crisis, Lex Luthor is initially older than Superman (old enough to be Perry White's childhood friend). Here, it's reversed where Lex appears to be younger than Superman and Batman.
Lex mentions his father being an immigrant from Europe. Lex's first appearance has him as the leader of a war-torn European nation.
Thomas Wayne was about to punch the mugger before being shot. In the Justice League Unlimited episode "For the Man Who Has Everything", and the comic story it was based on, Thomas fights Joe Chill in Bruce's Black Mercy-induced dream.
Young Bruce fell into a cave of bats during his parent's funeral, like in Batman Forever.
Bruce's first nightmare has a giant monstrous bat, akin to the Man-Bat. As well as the giant bat in a deleted scene of Batman Forever, which was used in the music video of "Hold Me, Thrill Me, Kiss Me, Kill Me" by U2.
In the movie theater scene, one of the movie posters shown is the 1940 The Mark of Zorro. This is the movie young Bruce and his parents saw that fateful night in the comics.
Doomsday crashed back down to Earth, and landed on Stryker's Island. In the comics, it's also the location of a maximum security prison.
Superman takes Doomsday into space during the fight, same as in Superman: Doomsday.
A TV interviewer asks Senator Finch "Must there be a Superman?" This was the title of a famous Bronze Age of Comic Books story which explored similar themes.
Batman's Training Montage is intercut with him in a lab experimenting with Kryptonite. In the earliest comic depiction of Batman's origin, he's succinctly depicted in two panels working out with a barbell and next in a lab doing a chemistry experiment.
Perry calls Batman "the Goddamn Gotham Bat-thing." Sound familiar?
Superman lacks the traditional spit-curl from other adaptations, instead being immovably slicked back. When he is affected by Kryptonite his hair suddenly becomes more pliable and droops down into the classic split-curl.
Metropolis and Gotham being twin cities separated by a bay goes back to the Bronze Age comics where this was the case.
At one point, it can be seen that the Batcomputer is connected to something called the "Oracle Network". This is most likely referencing Barbara Gordon's post-Batgirl identity, Oracle.
Another possibly unintentional one: Batman's cruel behavior towards criminals prior to Character Development is somewhat similar to Miller's modernportrayal of Batman.
In the film Lex Luthor creates Doomsday with a combination of Kryptonian DNA from Zod's cadaver and human DNA from himself. In the comics, the post-Crisis version of Superboy was created by Lex Luthor with a combination of Kryptonian DNA and Luthor's human DNA.
Like in Post-Crisis, Lex still has hair when Superman made his debut, and eventually went bald due to stress over his conflicts with Superman. This is also not the first adaptation to follow that same direction.
Word of God states that the scene where Clark travels alone and talks with a vision of Jonathan Kent in the snow is a metaphorical Mythology Gag to the Fortress of Solitude.
Bruce discusses with Alfred at one point that his ancestors made their fortune by trading raccoon pelts with the native tribes of Gotham. This was the same backstory behind the Wayne family fortune given in, of all things, a story arc in Batman (1966) involving Vincent Price as Egghead and a character named Chief Screaming Chicken.
"Is she with you?" "I thought she was with you." might refer to just who brought her in for the fight, but either of them being "with her" in another way has some backing, given in the comics Batman and Wonder Woman dated, while the DC Universe Animated Original Movies have her in a romance with Superman.
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