Let's try to keep fantasy out of it (LOTR). Science Fiction needs either some element of science or at least have thought-provoking speculation. LOTR doesn't fit that category, it is just set in a specific fantastical world.
Otherwise, I could nominate Crouching Tiger, Hidden Dragon. Or just about any martial arts fantasy movie with people flying through the air. It's outside of the realm of reality, but it's just the world those movies are set in. I could also nominate Il Mare or Ditto. But the time juxtaposition is just a setting to portray the romance. There's no science and there's no rumination or speculation on the meaning behind the fantastical elements.
Just one man's opinion.
My nomination: 48. Them. We need at least one radiation/giant bug movie right?