This is based on opinion. Please don't list it on a work's trope example list.
Tearjerker / Atlantis: The Lost Empire
Jim Varney died before the film was completed, and most of the production crew testify that he signed on knowing he wouldn't live to see the film's release. This, combined with the film's lackluster performance at the box office make the dedication to him doubly sad.
In the commentary the directors start to choke up a little bit when they remember working with him and refer to him as "That dear man."
Thankfully, they only needed a sound-alike to fill in for him for one line in the original movie.
As of 2015, watching the film and hearing the voices of the dear departed James Garner, Leonard Nimoy, Jim Varney, and Florence Stanley is pretty rough.
The expressions on the faces of the people in the prologue as they realize they're trapped outside the protective bubble, with the tsunami seconds from breaking over them. You can see couples holding each other just before the sea consumes the city.
For that matter, young Kida crying for her mother as she rises into the Crystal.
Speaking of Kida, the scene where she recounts what happened in the prologue to Milo. At first, the way she explains it starts out normally, but as soon as she brings up the crystal (or "star", as she thought it was) and subsequent loss of her mother, her voice significantly softens, almost as if even after all these centuries, it's still hard for her to talk about.
After the exciting battle with the Leviathan, Sweet setting a single candle in a helmet to drift on the water in the underground chamber, as a memorial to the many lives lost. Then Roarke comments they started with two hundred crewmembers, and they're all gone by the end of the movie...
The king telling Milo how he caused the destruction of Atlantis and the loss of his wife, and imploring him to save the city and Kida as he dies.
And since Leonard Nimoy died in 2015, this has become even sadder.
When Kida is released from the crystal, she comes out holding the bracelet her mother took off her (Kida's) wrist when the crystal took her. Given the implications, it's no surprise that Kida broke down in Milo's arms right after.