At the end of Ranmaru's story, Nobunaga comes all the way from Dragnor to congratulate him and tell him it doesn't matter what gender he is.
Similarly, No showing up to give Oichi a pep talk at the start of the latter's story.
The three versions of "Not Worth Fighting Over" have the friends reuniting and spending a day on the beach.
Somewhere in-between this and a moment of funny is the end of Yoshimoto's story, where he gets Kenshin and Shingen to play Pokemari with him.
Ujiyasu's story ends with him collecting the forty warriors he needs to hopefully ward off Kenshin and Shingen from invading Cragspur. However, the two show up and both congratulate him on his accomplishment... and it's revealed that all three are old friends. The epilogue says that the friendship the three had lasted the rest of their lives (and they're all shown fishing together).
A couple of the scenes where warlords link with legendaries can be like this. Mitsuhide practically gushes over Articuno, and Kenshin vows to help Mewtwo use its strength for good.
At the end of Nobunaga's story, he's accomplished his goal of uniting Ransei, and has his chance to destroy Arceus in order to stop the endless battles hurting friendships between humans and Pokemon. Then he realizes he's the only one to have actually seen the legendary Pokemon, and Arceus agrees to leave while Nobunaga spreads the tale that the legendary Pokemon is gone. After this, peace returns to the land.
A bit of fridge heartwarming- Keiji's link with Terrakion means that he was able to convince the Pokemon that humans aren't all bad.