The Memories movie series, even if you get the good ending can be heartwrenching.
Same with Love and Battle's final part, the good ending is both heartwarming and tearjerking. The person who you tried to convince that you are that person was trying to find you because you might disappear forever. As it turns out, you and your love had died a year ago.
When you first visit Driftveil City, you walk in on a dispute between an Ex-Team Plasma member who's undergone a Heel–Face Turn and a current member bent to Taking Over The World. The New Plasma member tries to convince the other to rejoin, and when the other professes how stealing Pokémon is wrong, the New Plasma member starts beating him up. It's actually surprisingly disturbing for a Pokémon game, and brings to mind images of gang bashings, made even worse by the fact that they used to be friends. Thankfully Hugh smacks the attacker away before things get too out of hand, but it's still incredibly depressing.
The Strange House, both Nightmare Fuel and a Tearjerker. Remember that ghost girl with her Abra on Marvelous Bridge in BW? This was where she lived and probably also where she died, having been killed by Darkrai who inflicted her with a "dark and endless dream". Just imagine how much she must have suffered since then, not only dying a horrible death, but also spending years on Marvelous Bridge waiting to return the Lunar Wing that could've saved her (it is implied that she was tricked out of it by Darkrai) to the Pokémon it belonged to; a Pokémon that would never come. After you pick up the Lunar Wing yourself, she sounds saddened that she can't return it herself anymore, but she says that it's OK and she asks you to return it instead. She then disappears, hopefully finding peace after so many years of pain and loneliness...
"Mom, Dad, Abra...Where are you?"
Fridge Horror sets in when you wonder if she was Darkrai's only victim in Unova? One must ask themselves how rare Lunar Wings are in the region and consider that someone is screwed if Darkrai gets to them. Also, given Abra is usually asleep, does that mean her Pokémon was afflicted at the same time she was?
There's a house in Icirrus City that can only be accessed in the winter time, and there's an Ace Trainer in there who is actually the sound designer, and if you answer yes to his question, he changes the music to that of Route 10 from the original games. That music can be a Tear Jerker on its own, especially since Route 10 was destroyed in a landslide on Victory Road and can no longer be accessed. The music changes back to normal when you leave the house, though.
There's an old man in one of the hotel rooms in Driftveil City. He mentions that Team Plasma convinced him to release his Pokémon, and since then he's been living his life on the road, staying in hotels around the country. He admits to being lonely without his Pokémon, but he thinks living alone is better than leaving his Pokémon behind when he dies. In other words, he chose isolation over causing his loved ones pain.
Hugh's backstory of how Team Plasma stole his little sister's Purrloin and he was helpless to stop them. It especially heats up after you and him defeat Zinzolin and a grunt in the Plasma Frigate, where he says that the Purrloin was caught by his late grandfather. And before you battle the Shadow Triad, it's revealed that it evolved into a Liepard. Then this quote after you defeat them and they leave:
Hugh:... ... Hey... <player>... If we let Team Plasma do what they want... There'll be more sad Pokémon like Purrloin and Kyurem...
It gets worse: the Liepard in question has become so indoctrinated by Team Plasma that it will only listen to and obey the Shadow Triad. All the years of effort Hugh went through to get his sister's Pokémon back, and it won't even listen to or acknowledge him or his sister anymore. Even after the Triad and Ghetsis' defeat, Liepard proves to still be fanatically loyal to Team Plasma alone.
Fridge Brilliance: Purrloin's evolution more than likely triggered its personality change. An early episode of the anime has Ash warned that if he uses a thunderstone to evolve Pikachu, his personality could be forever altered. Charmander's personality change when it evolves to Charmeleon later on proves this to be true, as like Liepard, he became disobedient.
But they eventually adapted to the new personalities. In fact, he Liepard can be seen out of its Poké Ball some time after the post-game, finally warming up to Hugh's little sister and happily allowing her to pet it.
During the cutscene in Giant Chasm, Ghetsis is using his cane to mind control Kyurem.
Ghetsis's breakdown after you defeat him. Immediately after the battle ends, the Shadow Triad comes by his side and tells you that he is no longer in a fit state to continue, speaking for him. When you remember his explosive rambling after his defeat in Black and White - "I'm absolutely perfect! I AM PERFECTION!" - it makes you wonder if that downfall impacted his psyche so badly that being defeated a second time was the final blow to his mental stability. For all the monstrous things he's done, it really adds a rather tragic fragility to his character, making one wonder what exactly could have happened to him for him to feel that the only way to validate his ego is to take over the entire world.
The ending of the "Everlasting Memories" movie is this. Even picking the right line choices will make the audience cry.
In the post-game, you can take on a favor by a couple in Humilau City to ring the bell at the Celestial Tower for them. Unfortunately, you have to take on four people in order to ring the bell, and all of them seem to be troubled in some way, showing frustration at how you are selflessly doing a errand for people you don't even know and try to stop you. Sure, they calm down and understand later, but there is something unpleasant about being on the receiving end of what they say to you and get a Revive from the couple after returning even though the bell sound doesn't reach the City and even feel sorry for them. What makes it worse is that the four are trainer classes you'd least expect to be mean: a waitress, a nursery aid, a clerk, and a maid. Their names are as follows: Jan, Ilse, Lana, and Tammy, respectively. Put their names together, and it spells JILT. And before you ask, a similar situation exists with their Japanese names—assembling the first syllable of each of Monami, Tokiko, Kanade, and Nozomi gets you "motokano", or "ex-girlfriends". Congratulations, you've just completed Pokemon's first infidelity-themed quest!
It gets even more complex. Each trainer specializes in a single typing which may or may not be symbolic in itself: Jan with three Level 60 Fire typesnote burning hate, Ilse with 4 Level 62 Normal typesnote Nothing left, Lana with five level 64 Ice typesnote Cold-hearted, and Tammy with six level 66 Steel typesnote heart is hardened. And at the top of the tower, if you've been to the Cave of Being, you encounter Mesprit, the embodiment of Emotion.
Early in Black and White, you meet a Roughneck who mentions he cannot seem to beat the Striaton Gym. In Black 2/White 2, you can talk to him again and learn that he still wasn't able to beat them and won't get to enjoy the badge because the gym closed.
If you're playing as a girl, the Ferris wheel date in Autumn is a Hiker who talks about something that happened in the summer two years ago, which really left him upset. He's vague on details, but he talks something about a lost loved one (implied to be the male hero of the previous B/W, who could meet the same Hiker during the summer). He even feels that he can only tell you and not other girls. And for the type Hikers usually are, being all jolly and everything, it's hard to not feel bad for the guy.
Several Ferris wheel dates across both games can get this feeling. The girl's winter Ferris wheel date, Guitarist January, tells the tale of how she was discovered for her music, but they have completely tried to change her image and sound. So now, she may live her dream, but you're the only one who she can be her true self around, and sing her true song, about an incompatible touch of love, using Normal vs. Ghost type as a metaphor. She also makes several last second word swaps when talking to you. It may read like a case of Hide Your Lesbians in the story.
The boy's winter date has a sad story as well. She mentions she has to constantly be on the run from someone. It sounds like some agency is forcing her back to work (since she is a Beauty), but it seems much worse given she is actively keeping her distance and mentions them "getting tougher" and having to train more. She's afraid to even look out of the window, thinking it'd be dangerous to do so. It's really impressive how terrifying and tear-jerking the backstories of the Ferris Wheel dates are in comparison to B/W's.
The ruins of N's Castle. It used to stand proud over the Pokemon League, but has now collapsed underneath, become nothing but a ruin of broken truths and ideals... just like N himself.
Think N's room was bad in Black/White? It's even worse to look at here, because of all the damage done to it by the falling debris. The toys are now scattered everywhere, now showing signs of not having been played with in a long time (as opposed to the first games, where they'd only recently been played with.) The music box track is now off-key and distorted, further driving home the image of an abruptly abandoned childhood. And N, who accompanies you the first time you visit here, actually has to leave the room because he can't stand to look at it for more than a few moments.
It doesn't help that the first time you go through, you also finally get the last few details of N's childhood, making it all the more depressing.
The first time you come to Humilau City, you see a man and a woman playfully chasing each other in circles just outside the Pokemon Center. Now, go back there in the post-game, after you've beaten the Champion, and you'll see the man standing there all alone. He tells you to treasure every moment you have with your loved ones, because you may never get another chance to...
It gets worse when you wonder if that woman is now with the man who jilted the four previous lovers mentioned above.
When visiting the home of Hilda/Hilbert in Nuvema Town from the original Black and White, Hilda/Hilbert's mother mistakes you for her child and asks if you've found N again. What really brings on the tears is you never find out where the player ended up those two years after the original games.
Checking the PC, television, and the bed upstairs imply that Hilda/Hilbert hasn't been in the house for a while. The implications of that, plus the mother's dialogue when you first visit her, could be tear-jerking in itself.
The Strange ending to The Giant Woman 1. Normally, the disfunctional relationship and battle between the protagonist and Monica is meant to be comical. But win, and she is shown to be in legitimate emotional pain from being brushed aside so often. So, she runs away, leaving the protagonist to think about how things went wrong so suddenly. The fantastical elements never come into play, and we're left with the story of a relationship realistically breaking down. But at least she never becomes the eponymous Giant Woman.
Its cry and its kidnapping pre-evolution might give Gothitelle a rather poor reputation, but it becomes tragic when you read its Pokédex entry in these games.
It can see the future from the movement of the stars. When it learns its Trainer's life span, it cries in sadness.
Kind of puts Gothitelle's Yandere status into perspective—it just wants to make the most of the time it has with you...
Heck, Gothorita's new Pokedex entry explains the kidnapping thing in a tear jerking (though still creepy) way: