X-Men: When Wolverine questions the team's uniform, Cyclops sarcastically asks if he would rather dress in a yellow spandex (Wolverine's suit in comic books is yellow with blue ornaments).
X2: X-Men United: After Magneto saves the Blackbird, he says "When will these people learn to fly?", referencing the fact that several of the X-Men can fly in the comics.
In the comics, Deadpool's nickname is "The Merc with the Mouth". Here, he's the Merc with No Mouth.
Stryker's ultimate mutant weapon being called "Weapon XI", in reference to the revelation in the comics that "Weapon X" actually meant "Weapon Ten". Which means that if Weapon XI is Wade Wilson, and Weapon X is Wolverine, there were nine previous attempts.
Stryker can be seen wearing a silver cross necklace in the scene where he goes to meet Logan in the hospital, likely as a nod to the fact that he was a priest (not a military officer) in the comics.
Also, during the final fight, there's a brief close-up of Deadpool charging up his Eye Beams, which causes his face to resemble his comic counterpart's mask.
The team's original lineup includes an "Angel," but it's Angel Salvadore (a comparatively minor character from the comics) instead of Warren Worthingtonnote who, going by the movie-verse's timeline, wouldn't have been born at the time the film takes place.
A major character on the villains' side is revealed to have grown up with Xavier—although in this version it's Raven Darkholme (who's his foster sister in this version) instead of Cain Marko (who was his step-brother in the comics).
Shaw referring to mutants as "Children of the Atom."
Charles is quite protective of his hair.
The Nazi Gold is a nod to Uncanny X-Men #161, which told the story of how Magneto and Xavier first met and parted ways. The issue was one of several stories in the comics which inspired this movie.
