I think Citizen Kane will remain the first in future lists. It aged not so well, but we are talking about 66 years!
But aside its technical achievements, narratively it's almost a posmodern film, with a central character deconstructed in the subjective views of a group of different people who knew him in different moments of his life.
The only moment we get an omniscient view of the story is at the end, in the famous "rosebud" scene.
Someone named City of God. Very good movie, but a brazilian movie. If we were considering movies of all around the world for the top 100... well, it would be a massacre! I think almost 50 of the actual listed movies would have to let their place for other gems from different moments of cinema history and different places of the world.