Spider-Man 2 is adapted from If This Be My Destiny...! (Doctor Octopus' Origins Episode) and mainly Spider-Man No More! (dealing with Peter's 10-Minute Retirement due to the stress of his responsibilities), with a dash of Spider-Man: The Animated Series sprinkled in (Peter and Otto's student-mentor relationship). The element of Peter surpressing his powers because of the stress of his civil life is taken from The Amazing Spider-Man Annual 1 (which famously features the first appearance of the Sinister Six who kidnapped Aunt May and Betty Brandt. While no villain other than Ock appears here, he does in fact kidnap Aunt May).
Spider-Man 3 is adapted from The Amazing Spider-Man #136 (Harry Osborn succeeding his father as the new Green Goblin), The Amazing Spider-Man #4 (Sandman's origin story), Amazing Spider-Man #252 (Peter acquiring the black symbiote), Web of Spider-Man #18 (Eddie Brock's debut), Amazing Spider-Man #299 (Eddie Brock becoming Venom's host), and The Spectacular Spider-Man #200 (Harry's Redemption Equals Death).
The Amazing Spider-Man combines Peter Parker's origin story with the Lizard story, which never appeared in Spidey's origin, as well as elements from Ultimate Spider-Man (2000), mainly the fact that Oscorp was where Spider-Man got his powers from and his parents being scientists instead of super spies like in the mainstream comics.
The Amazing Spider-Man 2 combined the origin of Electro (60s story) with The Night Gwen Stacy Died (70s). Once again, the former villain is not present at all in the latter story, a story that involved Green Goblin (albeit this time HarryOsborn taking his father's place in the part). The Rhino for instance is a Russian gangster like his classic depiction, but pilots a Mini-Mecha/Powered Armor like his Ultimate counterpart.
Punisher: War Zone crafted a story that used both characters from the mainstream books and The Punisher MAX as it has Jigsaw as its Big Bad (though the Heavy, the villain of the Max arc, "Girls in White Dresses", which was released a few months before the movie, was revealed to be the MAX version of the character), yet the movie shows him interacting with Don Cesare as the movie makes Cesare Jigsaw's uncle; he's shipping in something for the Bulats; and Pittsy and Ink, (henchmen for Nicolas Cavella) and Maginty are shown working for Jigsaw. Likewise the movie also shows Martin Soap working with Paul Budiansky.
The original X-Men (2000) uses elements of the famous "Days of Future Past" storyline (though with the Time Traveladapted out), but it's also loosely inspired by the first few stories in the comics where the team fought Magneto. It's about the Brotherhood targeting Senator Robert Kelly, and it features the X-Men trying to stop Mutant terrorists from attacking a gathering of politicians, but it also features Magneto trying to overthrow the US government.note Magneto only appeared in the future portions of "Days of Future Past", where he played a heroic role.
X2: X-Men United combines the plots of the graphic novel "God Loves, Man Kills" with the original "Weapon X" arc. It features the Mutant-hating villain William Stryker plotting to kill the world's Mutants, but it's also about Wolverine attempting to unravel the secrets of his past. Notably, it reimagines the fanatical priest Reverend William Stryker as the military scientist Colonel William Stryker, and it portrays him as the man who gave Wolverine his adamantium claws—essentially making him a Composite Character of William Stryker and Dr. Abraham Cornelius.
X-Men: The Last Stand combines the plots of "The Dark Phoenix Saga" and the "Gifted" mini-arc from Astonishing X-Men. It features Jean Grey coming Back from the Dead as the murderous "Phoenix", but it's also all about the world's Mutants being divided by the invention of a controversial "cure" for mutation.
X-Men Origins: Wolverine adapts several plots from the comic in Broad Strokes, referencing parts of Wolverine: Origin, Wolverine's relationship with Silverfox, involvement in Team X, Barry Windsor-Smith's Weapon X, and Deadpool being part of Weapon X.
Logan is a loose adaptation of Old Man Logan in part due to rights issues with other Marvel characters. Additionally, it changes the deaths of the X-Men from being Mysterio tricking Wolverine into killing them to Xavier accidentally killing them with his powers during a seizure. It also adapts elements of Death of Wolverine, including Wolverine's healing factor shutting down and ultimately Wolverine dying, in a manner similar to Sarah Kinney's death in X-23's original comic. The modified crops Transigen created to kill mutants is a more grounded version of the depowering of mutants in House of M. Elements of X-23: Innocence Lost were also included, X-23 and her origins most notably, mixed with her original X-Men: Evolution incarnation. She has the age and implied ethnicity of her cartoon version, but the design and darker personality of her comic version (bar some changes to go with her decreased age, such as scrapping her teenage prostitution backstory).
The Incredible Hulk (2008), while officially mostly drawing from the comics; takes a lot from The Incredible Hulk (1977) live-action series. The origins of the Hulk, right down to the origin sequence, are near identical and the film has many homages. It also took a few cues from Hulk with some more comic elements also added in such as the antagonists.
The Avengers draws heavily from not only the mainstream Avengers comics, but The Ultimates as well. Loki is still used as the reason behind the team's formation, but a number of elements (such as Hawkeye and Black Widow being black-ops agents and founding members of the team, and the team being formed to combat an alien invasion by the Chitauri, whom Loki commands in the MCU) come from the Ultimate universe.
Iron Man 3 combines elements of the "Extremis" arc by Warren Ellis, most notably the Extremis itself and many characters from that comic such as Aldrich Killian, the "Sentient Armor" arc by Joe Quesada, the Mandarin's origin story, more plot points from the "Armor Wars" arc, "The Five Nightmares" arc with Ezekiel Stane, and the Civil War story.
Avengers: Age of Ultron incorporates Ultron and The Vision's intro story (Avengers #54–58), Quicksilver and Scarlet Witch leaving a terrorist organization to join the Avengers (Avengers #16) (in the case of the film, HYDRA, though Scarlet Witch orchestrates Ultron's creation and serves him with Quicksilver until he goes too far), the Sentient Armor story-line in which Iron Man created an AI suit that went insane and tried to kill him (Iron Man vol.3 #26–30), Ultron using multiple bodies (Ultron Unlimited), and the name of the Crisis CrossoverAge of Ultron.
Thor: Ragnarok is adapted from both the Thor: Ragnarok storyline, involving the Ragnarok on Asgard (this time with Hela taking a prominent role as the main antagonist) and Planet Hulk (the appearance of the planet Sakaar in the film, and the involvement of Hulk, Korg, and Miek, though Grandmaster is the one who takes on Red King's role as the planet's ruler).
The plot of Black Panther is largely drawn from Don McGregor's "Panther's Rage" arc from The '70s (Killmonger igniting a violent insurrection in Wakanda, which leads to a duel atop Warrior Falls that ends with T'Challa being thrown to his apparent demise), but also has story elements (Killmonger becoming the new Black Panther after seemingly killing T'Challa and winning the Wakandan throne) and major characters taken from the run by Christopher Priest (Nakia, Okoye and Ross) and Reginald Hudlin's (Shuri) respective runs. Some of the visuals (namely the new Black Panther suit) and at least one character (Ayo) were also taken from the very recent run by Ta-Nehisi Coates and Brian Stelfreeze.
Spider-Man: No Way Home takes the identity erasure plotline from One More Day (as well as the ending, where Peter is forced to sacrifice his romantic relationship with MJ) and combines it with a hint of Spider-Verse (where Peter battles villains from alternate realities and ultimately winds up teaming up with alternate Spider-Men from the Multiverse).
Eternals adapts the original Kirby series, but incorporates ideas from the Alternate Universe series Earth X, mainly the idea that the Celestials created the Eternals to guard a Celestial egg implanted on Earth, which is the primary source of tension in the movie, as opposed to merely "the Celestials are coming to judge Earth".
Ultimate Marvel adapts, reformulates and mixes elements and stories from all the long history of Marvel Comics. From the Fantastic Four to Cable, from Galactus to the Clone saga, anything is fair game.
Part 2 adapts The Amazing Spider-Man #136 (Harry Osborn succeeding his father as the new Goblin, in this case Black Goblin), The Amazing Spider-Man Vol.1 #257 & #258 (Mary Jane uncovering Peter's Secret Identity), The First Clone Saga (Ben Reilly's introduction, Miles Warren cloning Gwen Stacyfor himself), and The Night Gwen Stacy Died (the obvious, Peter and MJ getting closer).
Part 3 adapts the first Secret Wars (the chapter opens with Peter participating in said war) and mostly Kraven's Last Hunt, with the ending taking heavy cues from Amazing Spider-Man #299 (Venom looking for a new host after parting ways with Spidey, in this case Kraven the Hunter).
Part 5 adapts The Amazing Spider-Man vol. 2 #30 (Morlun's introduction story), Spider-Man: The Other (Morlun hunting for Peter to feed on him), Civil War, and Spider-Girl (Peter and MJ's daughter becoming her own superhero).
