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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.
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.
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.