The "X-Men 1.5" Director's Cut has a blink-and-you'll-miss-it Deleted Scene from X-Men where the energy pulse from Magneto's device washes over the X-Men. Jean Grey is the only one who shows a physical reaction to the flash; this would seem to be the event that activated the Phoenix Force which would become so important in the next two movies. The second film acted as if this scene had been left in, with Scott and Jean discussing how her powers had changed since the Statue of Liberty.
In X2: X-Men United, when Professor X is having difficulty trying to get a lock on Nightcrawler, Logan flippantly asks if he can't just concentrate harder. Xavier replies dryly, "If I wanted to kill him, yes." Later Stryker gets Jason to brainwash Xavier into doing precisely this - only on a much larger scale.
Stryker says to Wade Wilson that he'd be the perfect soldier if he didn't have such a mouth. Stryker later turns Wade into a mutated super-soldier who literally has no mouth.
Kayla gets a man to back off from a confrontation with Logan, attributing it to "female powers of persuasion." She earlier fails to convince Logan not to confront the man in the first place. She's using her mutant power, which doesn't work on Sabretooth either—also hinting that her feelings for Logan are genuine since she can't just make him fall for her.
When we first see Erik as an adult, he uses his powers to slam a coin at a picture of Shaw in the forehead. This is how he kills Shaw in their final confrontation, except much slower.
Also part Chekhov's Skill where Erik asks Charles to shoot him point-blank, and when met with Charles' refusal, he states he can deflect it. This comes back at the end where Moira shoots at Magneto to stop him from sending the missiles back at the American and Russian navies and he easily deflects the bullets ... only to have one bullet hit Charles and paralyze him.
And in a scene where Havok is learning to shoot straight in the bomb shelter, Charles and Hank are standing right to either side of the target manekin. Charles says, with light emphasis, "And try not to hit ME, there's a good chap". A little odd, considering Hank is just as likely to get hit, so it should be "us". Later in the movie, of course, Charles is hit by a bullet, due to standing right NEXT TO its intended target, Erik.
Before the attack at the CIA base, Havok beats Darwin at a pinball game. Darwin declares "Jesus man, you're killing me!" Later, Shaw uses the energy absorbed from Havok's blast to kill Darwin.
One of the earlier modern day scenes in the film features Logan delivering some punishment to a hunter who supposedly used a poisoned broad-tip arrow to hunt the former's grizzly bear companion. Poisoned arrows reappear in the third act, when Harada uses a poisoned arrow to knock Wolverine out for the climax.
Yukio's vision of Wolverine's future, although it doesn't play out quite the way she saw it. However, it becomes Double Subverted, as director James Mangold has confirmed that Yukio's vision is finally fulfilled in Logan, in a symbolic way.
Noburo's remark about the Yashida's expensive adamantium research.
The fact that Yukio didn't foresee IchirÅ dying that night.
"She can transform into anyone. A general, a secret service man, even you, Mr. President."
When Wolverine is flashing his claws to Magneto, he says the line "Imagine if they were metal." Wolverine would later get metal claws and Magneto is seen taking control of Wolverines skeleton multiple times in the earlier films.
Mystique's line when the Vietnamese general is hitting on her.
General: A pretty girl interested in politics... Mystique: Looks can be deceiving.
After Deadpool counts down his 12 rounds in the opening fight sequence, he puts the muzzles of both guns up to his nose, inhales the cordite, and says "I'm touching myself tonight." Not long after that, he cuts off his hand to escape Colossus, returns home, and tells Al that she may want to leave the room after she comments on the size of his hand.
Wade:[whispering to Al] I bet it feels huge in this hand!
When Deadpool, Colossus and NTW confront Ajax and Angel Dust, Ajax tells Deadpool to Say My Name (a Call-Back to Wade's "activation" in the workshop). Deadpool mutters "Imma spell it out for you." After dispatching the group of mooks, a shot from Ajax's viewpoint shows Deadpool standing next to the bodies of nine mooks, arranged to spell out "Francis". The letter "I" is dotted with a mook's severed head. And one of the corpses is mooning him.
Ajax[to Vanessa] Does he write you notes, too? He's such a romantic!
When Xavier is giving Laura a meal, Laura - who is sitting down - easily stops Logan from taking her backpack in a tug of war.
One of the Laura's X-Men comic books (specifically created for the film) have the X-Men attending a burial. The film gives you two burials (Charles and Logan himself) in addition to the funeral service seen at the beginning.
An example that doesn't even happen in the movie. A short film, Deadpool: No Good Deed (which aired right before Logan during the film's theatrical run) ends with a heavily modified rendition of The Old Man and the Sea. In the film proper, Logan wants to buy a boat so he can take Charles offshore and prevent him from hurting anyone again with his powers.
Invoked and lampshaded by name in the Ice Box scenes where they mention "the monster" kept in solitary in the basement. The only real surprise is which "monster" from Marvel canon it's going to be. Surprise, it's a new Juggernaut!
A more traditional example occurs during the "Change the Uncomfortable Subject" conversation documented above. Deadpool comments that he wishes he could turn back time and apply a Reset Button to the conversation... which, subsequently, happens.
There's a little one in the scene that establishes how Domino's powers work, when kicking the driver out of the truck causes a side mirror to spin around. It doesn't trigger anything at the time - then Cable catches up to the truck, uses the BFG and lines up a direct shot, at which point the side mirror sends the sunlight right into his eye.
that Yukio's vision is finally fulfilled in Logan, in a symbolic way.