Although the series had a number of touching moments, the latter half of the final episode was one long bout of tear-jerking.
Episode 5: Little Marie tells Nadia and Jean about how her parents were shot by Gargoyle's soldiers, ending her recollection in tears. Later, Nadia and Jean dig graves for Marie's parents, and tearfully reveal to the little girl that she'll never see her mother, father, or pet dog again. The episode ends with all three weeping at the graves, with Marie lamenting, "I want to go to Mama and Papa!"
Episode 15: The climax of this episode involves a genial sailor, Ensign Fait, sacrificing his life to save the Nautilus both from a lethal gas leak and from being captured by the American battleships. What makes this moment truly heartwrenching is how Jean gradually becomes crushed when he vainly argues for the sailor to be rescued. (Fait's death scene, incidentally, is truly terrifying, in which the sailor coughs uncontrollably to his death after screaming "Oh no! I don't wanna die! There's so many more things I wanted to do!" right after he told Jean that it was okay because he lived a good life. To have him completely contradict that right after, and in such a desperate manner, made this a huge Tearjerker.
Episode 16: The entire episode involves a trip to the Atlantis graveyard, in which the heroic sailors are laid to rest. Here, Jean discovers that his father has been killed by Gargoyle. As if he hadn't already been brokenhearted, he becomes extremely depressed and even considers giving up inventing. Then, in a Crowning Moment of Heartwarming, Nadia, genuinely worried about Jean, comes by and tries to comfort him; the episode ends with her weeping on his shoulder while they stand beside the funeral.
Episode 22: Electra's entire flashback scene. And the ending of that episode.
Episode 35: Nadia tearfully reveals that she feels like a totally selfish, unloveable person and tries to commit suicide to escape from her fate. Instead, she is gently lowered to the ground by her Blue Water ala Sheeta's crystal in Castle in the Sky (although this is revealed, not seen). Her friends are all traumatized by what she has done (Grandis slaps Nadia across the face, while Sanson calls her out for "playing this tragic little game of yours!"), but Jean kindly tells Nadia that he doesn't care about who she thinks she is, or even about her origins as an Atlantean—he loves her anyway. Nadia is so moved that she tearfully apologizes (perhaps also for other unkind words/things she said/did to him too). Later, they discover that it's Nadia's birthday and have a wonderful celebration.