Following the success of the 2000 movie, the X-Men switched to dark leather costumes which more closely resembled those of the movie. The leather uniforms only lasted until 2004, when Joss Whedon had the team return to more traditional superhero costumes in Astonishing X-Men.
Toad's markedly different appearance and advanced powers from the first movie (a mostly regular-looking guy with a prehensile tongue and amazing acrobatic skills as opposed to a deformed hunchback who just jumps around a bit) were also copied, with the changes taking place in the 2001 X-Men Forever limited series. That same story also had Mystique adopt her scaled, reptilian appearance from the movies, with both characters' new looks brought about by an accident involving an alien regeneration device. While Toad ended up keeping the tongue and acrobatic abilities, Mystique went back to her classic appearance not long after.
As a minor example, Rogue used to have a white skunk stripe, across her head from front to back. Ever since the movies, only her front bangs have been white (even in X-Men Forever, where her original hair style, at least at first, should have been retained).
Rogue also lost her curls in favor of straight long hair similar to Anna Paquin's. In fact, in a couple of issues it's clear that Paquin herself◊ is used as a reference.
Rogue's real name, Anna Marie, was also taken from the movies, where she was Named by the Adaptation. Later writers (such as Mike Carey) also gave some of the cinematic Rogue's angst to her comic counterpart.
Many artists since 2000 showed Wolverine's claws coming from between his fingers as opposed to the backs of his knuckles. Also, like the Superman example, some artists have drawn Wolverine looking like Hugh Jackman.
It may shock people to learn that the idea of the Xavier Institute as an actual school for mutants outside of the X-Men was also something that came from the movies. Originally, while the school aspect was part of a cover story, and the only students were the X-Men themselves, because most of them were a bunch of teenagers that still needed an education. It being a school for mutants who are not X-Men was, however, a creation of the films. Then the first movie came out and introduced the idea of the Institute as a real school with numerous mutant students, and Grant Morrison subsequently made the idea canon in the comics.
Magneto was originally depicted as being resistant to Xavier's telepathy, with it being implied that he possessed latent mental powers of his own (though some stories suggested that special circuitry in his helmet might also be the cause of this). During the "Riot at Xavier's" storyline, Morrison canonized the first movie's idea that Magneto's telepathic immunity came from his trademark helmet, a stance the comics have maintained since then.
From the classic Age of Apocalypse, we've got the classic Sunfire later sporting his AoA counterpart's look, ironically as a Horseman of Apocalypse. Earlier than that, Kitty Pryde briefly employed a claw device similar to the one used by her AoA self.
During Age of Apocalypse, mutants were classified as Alpha or Omega level (apparently the difference between mutants with a useful combat power and Mutants of Mass Destruction). This made sense in the Darwinian dystopia Apocalypse was running, but the terms migrated back to the main Marvel U for no apparent reason.
For a time, Lady Deathstrike was redesigned to resemble her counterpart from X2: X-Men United, complete with exposed hair (as opposed to the brown cap with red strips of fabric she wore on her head for many years) and a black leather outfit. She was also Retconned into being William Stryker's close personal friend and enforcer, despite the two never having met on-panel before that point. While her black costume was eventually done away with, her movie-inspired hairstyle stuck around, and is still used in most of her modern appearances (such as in Weapon X (2017)).
Likewise, years after X2 dubbed Stryker's previously-unnamed son "Jason," Brian Michael Bendis canonized the name when he brought the character back in All-New X-Men.
Due to the popularity of X-Men: First Class, Marvel launched First X-Men, a prequel series about an early incarnation of the team led by Magneto and a not-yet-disabled Professor Xavier. However, it seems plans changed, as Xavier and Magneto ended up as Advertised Extras; the team was actually led by Wolverine and Sabretooth.
Gambit's role in X-Men Origins: Wolverine led to the Weapon X: First Class mini-series, which established that as a teen, Gambit was present at the Weapon X facility the night Wolverine made his fateful escape.
In X-Men Origins: Wolverine, Logan voluntarily goes through the Weapon X process. In Sabretooth Reborn a flashback establishes Logan did volunteer for the process, and the memory had been forgotten. That entire run entered Canon Discontinuity soon after, so it's not clear if this is still canon.
After being resurrected in the comics, Wolverine gained the ability to heat up his claws. According to Charles Soule, this power was inspired by some of Wolverine's moves from the Marvel vs. Capcom games.
The second (and more familiar) uniform that Wolverine sported in the Ultimate X-Men series was later worn by the mainstream Wolverine briefly outside of New X-Men, and by the Wolverine of X-Men: Evolution in the final two seasons.
In the original comics, Iceman was a founding member of the team and about the same age as Cyclops and the other X-Men. The movie made him a teenage trainee who was significantly younger than the real X-Men, and this eventually carried over into Ultimate X Men and X-Men: Evolution.
Sabretooth's post-AXIS design draws some inspiration from Liev Schreiber's portrayal of the character in X-Men Origins: Wolverine, namely the shorter haircut, mutton chops, and less bestial appearance.
Jean and Cyclops got married because of a planned plot from Season 2 of the hit X-Men: The Animated Series animated series. Interestingly, Bob Harras also asked the writers of the cartoon to hold off on having them tie the knot for real, which is why in the show, the wedding turned out to be the work of Mr. Sinister.
Negasonic Teenage Warhead was redesigned in the Deadpool & the Mercs for Money series to resemble her counterpart from Deadpool (2016). An issue of Marvel’s Voices (2022) also established that Negasonic is a lesbian like she was revealed to be in Deadpool 2, and introduced a new character named Yuki Ohara that's a canonized version of that movie's very different version of Yukio.
In Ultimate X Men Wolverine joins the X-Men with the secret mission to kill Charles Xavier. A similar thing was revealed to have happened in "Wolverine Origins" #29. However, mainstream Wolverine did not have a Heel–Face Turn like the Ultimate one: Xavier let him in, fully knowing about his mission, and then used his powers to alter his mind into working for him instead.
After X-Men: Days of Future Past boosted popularity of Blink, the main universe version (not the Exiles version, who is popular but seldom used) began wearing her hair in a plaited ponytail over her shoulder like the movie version did.
First off, there's their codename. In the comics, it was "Changeling", but when the show started, the Teen Titans character Beast Boy was using it, so they were renamed to "Morph", which went on to be the codenames of their Age of Apocalypse and Exiles incarnations.
Now, with Sequel SeriesX-Men '97, Morph's appearance has changed to resemble the AoA and Exiles versions: bald, noseless, blank eyes, and off-white skin.
◊ is used as a reference.
