These are all movies that celebrate science, skepticism, and rationality. In some, the heroes save the day using science or rational inquiry. In some, the bad guys use mysticism, woo, pseudoscience, or religion for their own, evil or misguided, ends. Some are non-fiction that use the medium of entertainment to teach or encourage critical thinking, rational inquiry or science. Some movies may use a "magical" component as a story-telling device, but in a universe that is internally consistent with that magical element, the features still include using rational thought & critical thinking as a positive force in the plot. Some just poke fun at irrational or illogical ideas.
What this list does NOT include are movies that show science out of control, or mad scientists "playing god" and ending the world (i.e. Jurassic Park), or movies in which the science is so bad, that it ruins the enjoyment of the movie by those who have even a mild understanding of how the universe works (and that might be a subjective judgement).
These are all movies I have personally watched and verified for the required criteria. Others may exist that I have not seen. If you know of a movie or show that you think should be on this list, you can ask me to review it. Making a suggestion here in the comments makes that movie title visible to anyone who visits this list, even if I haven't watched it yet and haven't added it to this list, so making suggestions here only makes this list more comprehensive & more valuable for the skeptic community looking for movies to watch. So please, recommend away!