Wolverine and Rogue. Every time they interact is one heart-warmer after another. But the best, by far, would have to be when he comforts her on the train.
Well, possibly not when she wakes him up from a nightmare and Logan stabs her with his claws and they almost kill each other. But it leads to the bit on the train, which is heart-warming.
Even then before he realized her power, his first reaction was to call for help when he stabbed her. Even after she uses her powers to steal his healing ability, the first thing he asks before waking is if she's alright.
The fact that he stabbed himself to free himself in order to save her is worth mentioning. Because of his super hearing her crying for help is what set him off in the movies equivalent to his Berserker Rage.
To take it further, when he finally gets to her and sees she's unconscious, he rips off his glove and touches Rogue, trying to transfer his healing abilities to her. When it doesn't seem to work, he simply cradles her against, almost like a father would to his daughter.
When they first meet, Rogue is hitching a ride on Wolverine's truck. At first he makes her get out and goes to drive off...and he doesn't even make it five seconds before he stops the truck and lets her get on. Then he gives her some food when she asks if he has any, since she's obviously starving.
Cyclops telling the professor how much of a father he is to him after Mystique poisoned him via Cerebro: "You've taught me everything I know that's worth knowing... If anything should happen... I'll take good care of them."
Becomes a bit Harsher in Hindsight after he's killed near the beginning of X-Men: Last Stand.
After seeing Jean using Cerebro - which, as was earlier made clear, is dangerous to her due to her lack of training - Cyclops runs as fast as he can to the chamber only for the doors to slam shut in his face. When they reopen, she's on the floor, barely conscious, and Scott is almost crying with worry.
Another Scott and Jean one: After Magneto has used his powers to pin them to a wall, his visor lost and his face facing hers, she tells him to open his eyes as part of a plan to escape - to which he replies: "No, I don't want to hurt you." And he refuses to open them until she gives him a single, heartfelt "Trust me."
Despite the opposing philosophies that have them figuratively and literally at war with each other, there is still mutual respect between Charles and Erik, especially since Charles refuses to give up bringing Erik to his senses. Charles is even kind enough to keep Erik company when the latter is finally imprisoned. Charles' retort that he will always be there in reference to Erik's unending determination to fight his war is a threat, it can also be seen as one old friend reassuring another.
Bobby using his powers to stop Pyro from throwing a fireball in Class, showing he cares about being an X-man, and a good person.
Bobby making an ice rose for Rogue, to feel welcome as student.
The famous Throw It In! where the kid stares and can't stop smiling at Cyclops, who is the child actor's favorite X-Man in real life.
It's brief, but moments before Senator Kelly turns into water, he has a conversation with Storm. The man is afraid of what's happening to him and begs her not to leave him, grabbing her hand. She holds it as he asks if she hates him and other homosapians. Just before dying, he tells Storm that she has one less person to hate.
