The cutscene for 100% Completion: The area masters all show up at the Sky Pavilion to thank you, and a quadruple rainbow crosses the sky. Awww!
In the sequel, just as Pikachu breaks down while trapped alone in the alternate version of Cove Town, Reshiram and Zekrom drop off Piplup to cheer Pikachu up.
Also in the sequel, Krookodile has a very poorly hidden crush on Audino. If the photos in the credits are to be believed, they've hooked up by the end! Awww.
After Darkrai repents himself and pulls a Heroic Sacrifice, the heroes take pity on him and go on a lengthy mission to rescue him. After Reshiram and Zekrom finally retrieve him, Darkrai is forgiven by the others and gets, as he wanted, real friends.
Litwick's PokéPark Pad entry: "Litwick love Chandelure's dance. They are worried that they may absorb someone's vital energy if they dance." Considering the Pokémon's reputation for stealing souls with gleeful abandon in past games, it's quite sweet.