All spoilers are unmarked!
The LeafGreen Run:
- Spuds and Barb adopt a Togepi egg at long last, since Nidoqueen's inability to breed meant they couldn't have kids of their own.
- Although it was meant as Rule of Cool, Junior hatching already evolved into Togetic implies that he's beyond maximum happiness with them.
- Pretty much everything involving Spuds and Barb. Special note goes to the end of the Christmas Episode and their aforementioned egg adoption.
The HeartGold Run:
- Lance offhandedly mentions that, because of the radio waves at the Lake of Rage, his Dragonite attacked him with Hyper Beam in a trance. Cut to a few minutes later, the radio wave is fixed, and Dragonite demolishes the hideout with Hyper Beam, and he tearfully embraces with a comforting Lance.
- Locke's reunion with Broseph, who as it turns out, survived exploding—turns out exploding just makes more Geodudes.
- When Morty gets a call after the Legendary Beasts awaken, he starts out serious, but at the end, quietly adds a little "I love you too" to the person calling and blushes when Locke takes notice. Who was calling? Eusine, who as it turns out is Morty's boyfriend here.