All Dogs Go to Heaven (Charlie)
Cats and Dogs: The Revenge of Kitty Galore (Diggs)
Downfall (Hitler's German Shepherd, Blondi)
K-9 (Jerry Lee, played by Koton, a real police dog)
Beverly Hills Chihuahua and its sequels (Delgado and his sons, Antonio and Alberto)
It's not really a movie, but Ginga Nagareboshi Gin features a German Shepherd named John. It's sequel, Ginga Densetsu Weed features a Shepherd named Jerome.
Bolt the title character from Bolt
The Hills Have Eyes (1973) (Beauty and Beast)
Bad Moon (Primo)
Rin Tin Tin
Trixie Uker from Homeward Bound II
Thunderbolt from 101 Dalmatians 2
I Am a Legend features a GSD
Underdog featured 3 GSDs.