There are so many good movies it's extremely hard to choose, but I'd probably go with:

Guillermo Del Toro's Pinocchio

Puss in Boots: The Last Wish

Bicentennial Man

The Last Samurai

The Phantom of the Opera

Honorable mentions:

The Lord of the Rings: Return of the King

Idiocracy

Office Space

Anne of Green Gables

Back to the Future

The Princess Bride

Django Unchained

Gladiator

Shutter Island

Various Star Trek Episodes which while technically not movies are incredible storytelling, including but not limited to:

Measure of a man

Who Watches the Watchers

The Inner Light

The Next Generation is the best series thanks largely to the great actor Patrick Stewart.