In no particular order - most of this is just me reading what's on my movie hard drive:
Blade Runner (Final Cut)
Planet of the Apes (original)
Invasion of the Body Snatchers (1978)
Raiders of the Lost Ark
Let the Right One In
Close Encounters of the Third Kind (Director's or Theatrical cut; just not the SE)
Das Boot (4.5-hour miniseries cut)
The Lord of the Rings Trilogy (1&2 Extended, 3 Theatrical)
Almost Famous (Untitled Director's Cut)
Back to the Future (the first one)
Alien (theatrical cut)
Aliens (theatrical cut, but ONLY because the scenes on LV-426 before the Marines land there shouldn't have been restored in the SE)
A Boy and His Dog
City of God
Pan's Labyrinth
Eternal Sunshine of the Spotless Mind
Kingdom of Heaven (Director's Cut)
The Fountain
Moon
The Fugitive
The Hunt for Red October
Jaws
Jurassic Park
Kiss Kiss Bang Bang
The Road
Office Space
Open Your Eyes ("Abre los Ojos" - was remade into the inferior Vanilla Sky)
The Wrestler
WALL-E
Toy Story Trilogy
Finding Nemo
The Incredibles
The Princess Bride
Six-String Samurai
The Terminator and Terminator 2 (either cut)
Thank You for Smoking
The Thing (Carpenter)
The Usual Suspects