Kitty practically Glomps Nightcrawler when they finally catch up to the ship he was traveling on.
Wolverine braving a fire to save a little girl, and then the little girl's parents want to help him afterwards, nice to see.
Both Emma Frost and Rogue'sHeel Face Turns respectively. Rogue reveals that she only joined the Brotherhood in order to infiltrate them, because she learned some unpleasant things from inside Toad's head. And it turns out that Emma wanted to stop the Phoenix from wiping out humanity, not help it.
In the Bad Future, the last things Magneto do are give Lorna his helmet and send her underground in order to protect her from the oncoming destruction. Magneto may not be the best father, but he still loves his kids.
Logan giving Jia Jing the codename "Sprite" (Kitty Pride's former title), telling her it's the name of his "favorite X-Man ever."
Quentin leaving the Jean Grey school so that he can help Idie in Issue #30.
Kubark returning to the school in the Annual.
Issue #40, when Scott and Wolverine come to terms for a moment while drunk.
At the graduation ceremony, Fantomex and SWORD director Abigail Brand are presented as the parents of Evan and Broo, respectively.
Plus, Captain America shows up for Quentin, a callback to their team up in A+X #4.