These are my favorite live-action family movies from 2000-2009. They are in alphabetical order and limited to 12.
http://www.ranker.com/list/movies-2000-2009-family-live-action/robg,
The Chronicles of Narnia: The Lion, the Witch and the Wardrobe
A Knight's Tale
Holes
Miracle
Nanny McPhee
Night at the Museum
Peter Pan
School of Rock
Shaolin Soccer
Harry Potter and the Sorcerer's Stone