This is based on opinion. Please don't list it on a work's trope example list.
Tear Jerker / Space Battleship Yamato 2199
Erich Domel's death, motivated by his will to not make his men's deaths senseless. The Yamato surviving, thus making everything a Senseless Sacrifice, only makes it worse.
"A Clockwork Prisoner": Analyzer re-activates a Garmillan android soldier in order to study it. He ends up befriending the curios automata, which he names "Alter". Later, Alter curiously peeks into the mainframe of the Yamato and finds a "goddess" (who is actually Yurisha) and goes to any length to pursue it. To protect the Yamato from a hack attack, Analyzer is forced to put Alter down. The episode, as a whole, goes to great lengths to explore the question of What Measure Is a Non-Human?.
How the war started in the series: the Gamilan ships appeared at the edge of the system for a peaceful contact when Serizawaordered to attack without even talking, Okita refused and was removed from command, and when Shima's father followed the order the Gamilans destroyed his ship and killed him. What's worse is that due to political necessities it was said that the Gamilans opened fire first, meaning that Serizawa got away with causing aHopeless War, the loathing Shima and many others have for the Gamilans is completely unjustified, and the Gamilans, who are trying to force Earth into surrender, have absolutely no idea why the Terrans don't do just that and refuse the demands of surrender they send before any engagement.
Earth three years after the return of the Yamato: once the environment was restored, the government went back on Okita's promise and started building ships with wave motion guns, using a time rift generated by the Cosmo Reverse to build the new fleet faster, and started a colonial expansion, and when Teresa of Telezart sent a request for help it was ignored, with Hijikata Reassigned to Antarctica for his efforts to have the Yamato mount a rescue mission. The crew of the Yamato rightly asks: where is the Earth they fought to restore?
How the crew of the Yamato answered to the situation above: they went to Telezart anyway, stealing the ship and committing high treason for justice, while also going back on Okita's promise and restoring their ship's wave motion gun to have a chance to succeed.