In Nimbasa City, after Bianca and her dad's argument (over whether Bianca should continue traveling), Elesa comes and tells them about how the trainers have Pokemon with them so they won't travel alone. Bianca's dad apologizes to his daughter for his selfish needs and for being an Overprotective Dad.
The music drives the feeling home - some fans who heard the music even before the context was revealed deemed it one of the most lovely music pieces in the game.
N's farewell. Just after you defeat Ghetsis at the end of the game, he tells you about how he couldn't believe how much your Pokemon loved you from the very start of the game.
Then we get one last close-up picture of him standing in front of the hole in the wall, bathed in light - and then he jumps through it and flies away on his Pokemon to freedom.
What's ultimately so heartwarming about this part of the story is that his life is turning over a new leaf. After a tearfully sadBack Story, he's able to leave his wasted past behind and start a whole new life. In a way, N is no different from a newborn infant - he's as innocent as a child and knows nothing about the outside world, but now he's able to discover it for himself and ultimately find a real purpose in life.
In Icirrus City in winter, you can enter a house where the Funny Foreigner grunt from Pokémon Gold and Silver lives. He reveals that he was planning on starting up Team Rocket again, but ended up not having time due to getting married and having a son. "But happy family is big hooray!" What makes it even cuter is that his son actually finds it cool that his father is an ex-Rocket rather than being upset that his dad once worked for the "bad guys."
The ferris wheel rides in general. For instance, when you play as Hilda, you ride with Aurora the Waitress in autumn. She tells you after the second time you ride with her that she doesn't have many friends, and that she cherishes her ride with you.
When you play as Hilda, you ride with Rich Boy Martin in the winter. The first time you meet him, he explains that he's sick and that he doesn't get to go out much. The second time, he comes back and tells you that he's really happy to have met you.
Ace Trainer Austin, who is terrified of the swaying ferris wheel (and admits it!), but is grateful that Hilda is willing to help him conquer it. Every time you ride it with him, he ends up at his limit and asks you to hold his hand.
Playing with Hilbert in autumn gives you Clerk Trisha, who at first gets scared of the height and tries to cuddle at your side. The second time she tells you she wishes she had a little brother like you. And don't mention her final dialog the last day of autumn...
It gets better in the sequel. Trisha is far happier and is a mother-to-be.
Bianca being reunited with her Munna. And the fact the player takes care of the grunt who stole it from her personally could count too.
This game goes to great lengths to ensure you know how strong the bond is between the three heroes, who in this case are childhood friends. Not only do you all three wait to be together to get your starter Pokemon, but Cheren and Bianca won't even step foot onto Route 1 until you've come to take the first step with them.
Alder's interaction with Cheren becomes this in hindsight. He causes Cheren to go through a Heroic Blue Screen Of Death at the realization his goal of becoming Champion was pointless if there was nothing more to it than that. Cheren ultimately comes out of it a better person, but we find out why Alder did this in the post game. His beloved starter Pokemon and him fought for the same reason Cheren originally did, but Alder didn't realize how empty his goal was until after his partner died, meaning he'd lost his chance to reach a more meaningful goal with his partner. Alder is trying to save Cheren from making the same mistake he did.
The last scene with the player, Cheren and Bianca before the player goes to the Pokemon League to stop N. Especially so when coupled with Route 10's music.
Take the four musketeers to the Moor of Icirrus. Reuniting Keldeo with the three Pokemon who raised it? Heartwarming and cute, all in one package,and it comes with an awesome new move for Keldeo.
One of the movies you can make in the sequels has your character using The Power of Love to reverse a curse on Monica, your sister/girlfriend. As Rosa, Monica turns back to normal instantly. But as Nate, Monica shrinks slowly, to the point that the epilogue mentions that she was finally back to normal after you had both grown old together.
The Skyarrow Bridge. The view, the music, the lack of danger... Everything about it makes it one of the most calming places in the entire series.