The end of the movie. Sparky's died a second time thanks to Mr. Whiskers dragging him back into the flaming windmill that then collapsed on him, so Victor, remembering what his parents tried to teach him the first time Sparky died, prepares to move on and simply accept Sparky within his heart... then Victor's father unexpectedly tells him that sometimes, adults don't know what they're talking about, and Victor's father sets up another lightning experiment using the townsfolks' car engines to try to bring Sparky back to life. It doesn't appear to work at first... But as Victor is turning to leave, Sparky suddenly wakes up and starts playing around with Persephone.
Victor's chat with Mr. Rzykruski over how his experiment worked because his heart was in the right place.
Really, once you get past his very creepy appearance and mannerisms, Mr. Rzykruski's relationship with Victor in general. The warmth that Martin Landau puts into the phrase "That is why you are scientist" when Victor says he still has a question is exactly how we'd want a teacher to be: Encouraging and genuinely helpful.
Nassor's desire to bring his pet hamster Colossus back from the dead does seem to have been sincerely motivated by love for a missing pet. Which, presumably, is why it worked and didn't simply turn the hamster into a hideous monster like the rest of the animals. At least, it worked until the idiot sent it up against the Gamera Expy tortoise.
Speaking of the tortoise, Toshiaki also seemed to bring his pet back to life not only for the science fair but because he truly missed him. The way he shouts "Shelley!" is just heartbreaking.
The many references to the history of animation in the movie, such as the stop-motion film Victor made in the beginning, and the Bambi Meets Godzilla scene. It really shows just how much Burton loves the medium.
Not to mention that the 1984 short and this film are very personal for Burton, since a lot of things in this suburban neighborhood echoes towns he grew up in.
Think about it this way: In 1984, the animated short got Burton fired from Disney. Fast forward over twenty years later, and the company basically pulled a 180 and said "You were right, we were wrong. Let's make this film." Who wouldn't feel a sense of pride in Burton's place?
During the baseball game, Sparky gets loose and catches one of the pitches. Instead of getting annoyed, Toshiaki smiles and says: "Nice catch, Sparky!"
This is emphasized because it's one of the few non-dickish things Toshiaki does or says in the movie.
The credit song "Strange Love" can inspire tears to those of the right disposition.