All of Beast's attacks (and his innate passives) are named after titles of famous novels. His recruitment information in the news feed was a paraphrasing of the famous opening words for Pride and Prejudice.
Fantomex's L1 move is named Diabolique, which is fitting since he is essentially a white-trenched version of Italian comic book character Diabolik, along with his sentient techno-organic ship E.V.A. being named after the eponymous protagonist's lover.
Fantomex's L6 move is named Fantôme, again referencing his roots as a partial homage to the classic character Fantômas.
Hawkeye's passive, Hawkeye's Initiative, is a shout-out to this Tumblr.
Hercules's news feed announcement, "Cool Story Bro!", referenced a meme originating from his comic book.
Hercules has five references to the Twelve Labors of the mythological Heracles in his attacks and debuffs (the Stymphalian Birds, Ceryneian Hind, Nemean Lion, Cretan Bull, and Cerberus were creatures he was sent to capture or kill). He also jokes in Spec Ops 4 that the task he was set (holding up a building for a while) was less boring than cleaning out the Augean Stables (another of his Labors). Another attack, "Rock of Ages," is a phrase from the Bible (though perhaps better known as a song title).
Squirrel Girl's 4th attack, Wrath of the Raging Squirrel, is a shout out to Akuma's Ultra in Street Fighter IV, Wrath of the Raging Demon, with the blackout and a barrage of attacks on the target.
When Tigra uses her Tiger's Fury ability, she adopts the same posture as Felicia from Darkstalkers does during the latter's taunt in Vampire Savior. Her Swipe ability animation looks a lot like Felicia's Rolling Buckler special move, namely the finishers (a sliding kick in Marvel vs. Capcom 2: New Age Of Heroes and the uppercut Felicia has since DS).
Union Jack's news feed announcement, "Once more unto the breach, dear friends", is lifted directly from a famous speech in Henry V. It's doubly fitting since the line is about trying again, and Union Jack's entire moveset is based on extra attacks from preempts and follow-ups.
X-23's L6 Move is called "Made for Walking", in a tribute to Nancy Sinatra's hit. To make the point extra obvious, the flavour text "One of these days..." (part of the chorus) is added under the move's description.
To Super Smash Bros.: One of the Prison Escapee Mook's attacks is labeled "Felon Punch!", with an appropriate attack animation.
The Yardbird Scrapper and Brute Bruiser mooks have a slam attack called "No Touching!"
Havok, Cyclops and Cable (aka Alex, Scott and Nathan Summers) have "Boys of Summer" as a team-up bonus. "Girls of Summer" is the bonus for Jean Grey and Emma Frost, Scott's love interests.
Before, bringing two mutants along (specifically, members of the X-Men) awarded the bonus of X-Force. It was later renamed Children of the Atom (also a novel of the same name involving mutants), while X-Force became a separate bonus, specifically for bringing in members of that team.
The third mission is called "Ultron Violence": likely a nod to "ultraviolence," aka murder, in A Clockwork Orange.
SpecOps 9 can be a loose adaptation of Iron Man 3, since it features Extremis, the release of alt. skins the Mark 42 and Iron Patriot, and Pepper in a prominent role (although the movie doesn't feature her actual alter-ego Rescue). Adding to the references is the new PVP bonus, the prominently pink "Limited Edition Watch".
When Nightcrawler faces Baron Zemo for the first time in Season 1 Mission 11.3, he alludes to Martin Luther's "here I stand" speech before the Diet of Worms. From Zemo's reaction, he either doesn't get the reference or just doesn't care.
Magneto opens up the boss fight of Season 1 Mission 11.5 with the greeting "Welcome to die, X-Chicken!" As it turns out, this Magneto is actually Mystique in disguise. The homage is even driven further with...
The first mission is titled "Lokasenna", referencing a old poem of the same name found in the compilation of Norse poems known as the Poetic Edda, is the beginning of the end for the various Syndicate villains' plan. Fitting, as the events of the original poem were said to have brought about the onset of Ragnarok, the end of the gods.
Marvel Ultimate Alliance. The roster of Marvel's best superheroes is further expanded given this game is always being updated compared to the finalized games in the PC and home consoles. Save for Iceman, most of the heroes from MUA are playable, while a whole bunch of familiar Masters of Evil villains from MUA showed up as well as members of the Syndicate.
Shawarma as a giftable item (it restores health and stamina and gives a "Well Fed" buff). In addition to being a cute reference to The Stinger of The Avengers, it just happened to come out on the same day How It Should Have Ended released their Avengers parody, which made heavy use of Shawarma.
"Das Boot", a shoe-based weapon for the Agent, is named after...well...