Misty: For somepony made of fire, I've never met a heart so cold. (cries)
"Portrait of a Princess": Pipp starts crying after she and Zipp are trapped in the cave, having been looking forward to having her portrait painted alongside her family.
In "Ali-Conned", Sunny is heartbroken when she realizes the ponies are only paying attention to her because of her Alicorn transformation. As the episode earlier notes, it is an all-too-painful reminder of her status before the events of the movie, where the whole of Maretime Bay treated her as nothing but a nuisance.
"The Traditional Unicorn Sleepover":
Izzy reveals that she is feeling homesick for Bridlewood, and wishes that she had another unicorn to be friends with.
Izzy is heartbroken when Misty leaves the sleepover.
" Have You Seen This Dragon?": Hitch's worry after Sparky goes missing.
In "Top Remodel", Misty feels so alone that she creates a Companion Cube by the name of "Madame Taffytail" to voice her increasingly conflicted feelings to.
In "The Jinxie Games", Queen Haven admits that she feels lonely now that her daughters are living in Maretime Bay.
"Sunny Side Up": Opaline's cruel treatment of Misty's reaches new heights when she uses her magic to literally ground her and place a barrier around the door to her room. Misty is left trapped, unable to do anything but reflect on her miserable lot in life.
"Missing the Mark"
Misty is overwhelmed by guilt when she sees Sparky's magic slowly being drained away by Opaline.
Everyone feels understandably betrayed by Misty in "Missing the Mark", and aren't quick to reconcile with her right away, even after she apologizes for her mistake.
"Cutie Blossom Bash": Misty spends most of the episode being deeply uncomfortable with the idea being put in the spotlight, but goes along with it for her friends. When she finally admits that she can't go through with ceremony, she's convinced that her friends will be disappointed in her.
The "Family Trees" two-parter has plenty of tearful moments.
All the flashbacks to Misty as a lost, scared little filly.
Hitch is fraught with worry over Sparky, who still hasn't fully recovered from being drained by Opaline.
Misty and Alphabittle are revealed to be father and daughter, and reunite in a powerfully emotional scene.
"Father of the Bridlewood": After trying to go along with all the activities Alphabittle brought her to, Misty finally breaks down and admits she hated all of it, adding that she doesn't remember any of the things her father says she used to love.
Misty: Whatever filly you used to love isn't here anymore. I'm sorry. I'm so sorry.
"Mane Smelody": A minor moment, but Sunny has a definite look of hurt on her face when she recalls how her original home (and most of the artifacts her father collected over the years) was destroyed.
"The Isle of Scaly":
Hitch is noticably torn over the idea that Sparky might be better off with his fellow dragons. Though he wants what's best for the hatchling, he can't help but feel sad over the idea of them parting ways.
Spike clearly misses his old pony friends, speaking wistfully of the time they spent together, and regretting having to seperate from them thanks to Opaline's attack.
"Roots of All Evil (Part 1)":
Just like in the previous generation, cutie marks are considered to be tied to a pony's very identity. When Opaline steals a pony's mark, they feel like they've lost a part of themselves.
Misty blames herself for Opaline's actions, feeling like the evil alicorn only got as far as they did because of her help.
Sunny also believes she's to blame, thinking she's still the same pony "stirring up trouble" she was before.
"Roots of All Evil (Part 2)": While all the Mane Six are affected, Misty is especially heartbroken when Opaline steals her cutie mark.
Secrets of Starlight: The Auroricorns have spent what may be years being forced to comply with Allura's demands, preventing them from living their lives and doing what they want.
