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Tear Jerker: Outlaw Star
The episode "Cats and Girls and Spaceships" from Outlaw Star, where Jim unknowingly kills the girl he had liked, and when she understandably fails to show up for their date afterward, he assumes she stood him up and never finds out the truth.
The girl has no idea she was fighting the boy she loved. And her last thought is she'll never be able to see Jim again.
The very, very end of the series, with the the whole crew reunited and setting off for new adventures, always makes this troper teary eyed, both because it's such a good send off and embodies the spirit of Outlaw Star, and because we won't get to see those adventures. The ending caption seals it.