This is based on opinion. Please don't list it on a work's trope example list.
Tear Jerker / Magical Pony Lyrical Twilight
Like the original show, Magical Pony Lyrical Twilight has Fate being punished by Presea for her failure. Unlike the show, however, the violence is on-screen and cringe-inducingly unpleasant. In some ways, it's even worse, since Fate was transformed into a pony only a little older than the Cutie Mark Crusaders.
Everything that happened in the past that was covered in Chapter 11. A unicorn noble named Somber managed to get married to Princess Aria of the Crystal Empire. After he married her, he used dark magic and love poison to control her and corrupt the entire kingdom. When the Princesses arrived, Celestia managed to free Aria from the love poison's mind control, but due to the fact that he had managed to make himself immortal, Princess Aria used her remaining power to give Celestia and Luna the power toseal him away. The worst part? Princess Aria was Luna's granddaughter. Then, the nobles of that time, led by Sombra's mother attempted to have Princess Luna charged with treason for killing Sombra (justified, since she had attempted to do exactly that) and for the Crystal Empire disappearing (unjustified, since it was Sombra's fault). Princess Celestia managed to stop this and suggested to Luna that she go to their old castle so that the nobles could cool down and forget about what had happened, but they not only didn't forget, but started spreading all sorts of nasty rumors about Luna, leading ponies to fear her night. When Luna found out about this, she wound up denouncing Equestria and becoming Nightmare Moon, bringing about the events described in the pilot out of jealous anger and hatred. Celestia, in an act of desperation, used the Elements of Harmony and gambled that they could return Luna to normal. Instead, they wound up sealing her in the moon.
Also, if you thought Presea's Cry for the Devil in the first Nanoha movie was sad, it was arguably even worse here. Due to having been healed by the Elements of Harmony, her fractured psyche was made whole again, and the realization of how she had treated Fate broke her so horribly, she had to be put on suicide watch. It just goes to show that sometimes, being Spared by the Adaptation can leave you a psychological wreck.
If you thought the condition the Book of Darkness left Hayate in during A's was bad, what it did to Trixie was much worse. It left her almost perpetually in a coma, to the point that in order to keep up the appearance that she's still going about her daily routine, one of the Wolkenritter, typically Vita, is forced to use magic to transform into her. It really brought a tear to this troper's eye, seeing the condition the Great and Powerful Trixie had been left in.