After spending an hour or so with Flickchart, here's what I've come up with. Potentially more detail on some of these choices later.
- The Dark Knight (2008)
- Almost Famous (2000)
- Training Day (2001)
- Children of Men (2007)
- Kill Bill Vol. 1 (2003)
- The Prestige (2006)
- Spirited Away (2001)
- Harry Potter and the Prisoner of Azkaban (2004)
- Memento (2001)
- Eternal Sunshine of the Spotless Mind (2004)
- Crouching Tiger, Hidden Dragon (2000)
- Wall-E (2008)
- Up (2009)
- Inside Man (2006)
- Anchorman: The Legend of Ron Burgundy (2004)
- Pan's Labyrinth (2006)
- Best in Show (2001)
- Signs (2002)
- The Royal Tenenbaums (2001)
- Sin City (2005)
Other movies of note for their pure repeatability or memorableness (regardless of quality): The Bourne Identity, Ocean's Eleven, The Matrix Reloaded, The Departed, Minority Report, Amelie, Little Miss Sunshine, Star Trek, Brick, Pitch Black, 25th Hour, Kung Fu Hustle, and 28 Days Later.
My least favorite movie of the decade that everybody seemed to love? Wedding Crashers followed closely by Meet the Parents and Borat.