It's tough to pick one's favourites from a great career that spanned 171 movies but, though I know that in many ways The Searchers and Stagecoach are the greatest of the Duke's movies, my five favourites are:
What are yours? Below the jump, some clips!
UPDATE: James Joyner joins the party. I second his endorsement of Rooster Cogburn.
From Red River:
She Wore a Yellow Ribbon: