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Tear Jerker: The Transformers
Poor Skyfire. Granted, G1's writing means there is quite a bit of Narm involved, but even so his story is heartwrenching. He was perfectly happy exploring the universe with his best friend... and then he crashed on Earth, spent the following nine million years frozen in the North Pole, was found purely by chance and had about five minutes of happiness at meeting his old friend Starscream again, then found out he was in the middle of a war, was immediately put to work by the Decepticons, realized he was working for the bad guys, got shot by his ex best friend when he refused to kill prisoners, and went down in a Heroic Sacrifice as soon as the good guys fixed him. All of this in a single episode. Poor guy needs a hug.
"We shall remember."
...and then he was resurrected 3 episodes later. *Cough*
Though I suppose you could call that last bit a happy tearjerker?
After a recent viewing "Desertion of the Dinobots" gets me. The Autobots are feeling somewhat melancholy at being refugees from Cybertron. In the second part, when Spike and Carly go there to get the Cybertonium and stumble upon a city in the underground and Spike says, "I wonder what this place used to be." And you realize how much the toll the Great War has taken on their civilization.
"The Golden Lagoon". Beachcomber has found a beautiful, Edenic little glade full of wild animals, untouched by the hand of man—and it contains a dangerous substance he knows the two sides will fight over if they find out about it. He spends the whole episode trying to prevent it, but the inevitable firefight happens, and both the glade and the substance are destroyed. The Autobots cheer because the Decepticons didn't get the stuff. The episode ends with Beachcomber sitting in the blackened crater of the glade, all the plants and animals dead, and mutters, "We won."
Seeing Optimus Prime fade to grey on his deathbed surrounded by friends in the movie was sad. Bringing him back to life just so we can see him unwillingly deceive and fight his friends and then be graphically blown up, piece by piece while he's still alive (the episode "Dark Awakening") was trauma inducing. Fortunately for fans, he was resurrected again at the end of the season. Unfortunately, the joy only lasted a few episodes; in the Japanese canon Prime died again, whilst in the West the whole series "died".
Optimus Prime: Monsters! They made me into a weapon, to destroy the very ones I loved in life. But you will save them, Rodimus Prime.
In "Nightmare Planet", the Quintessons kidnap a sleeping Daniel and hook him up to a machine that brings his dreams and nightmares into reality. Most are monsters that attack, but one is a fairy tale princess who helps the Autobots. When Daniel wakes up, everything that his mind created disappears, including the princess. Springer, who knew her the longest, mourns her.
In "Webworld", during the last act Cyclonus tries desperately to get the Torkuli to release Galvatron to no avail and has to watch helplessly as the planet enters his leader's mind to lobotomise him. He gets better in his CMOA. Galvatron pleading for his life and Cyclonus' help didn't help matters, a stark contrast to how he's been acting in the last two acts.