The trailer features two little scenes which were not used in the final film. In the first scene, which was probably cut from the sequence where Eleanor and Theo go through the house for the first time, they find a door, which they open, only to find a brick wall. The second scene is a piece of dialogue between Eleanor and Theo. Eleanor asks "Have you ever kept something to yourself because you were afraid?" to which Theo answers "All the time."
In Germany two versions of the end credits are existing: After the sign of "Dream Works" disappears the German theatrical and video and pay-TV version continues with the German dubbing crew and cast. The DVD version has only the end titles of the original version.
Theatrical release: When Theo and Nell meet Luke (just those three), Theo boldly asked Luke if he was gay or straight. Luke answered straight. I saw this film in the theater in the first week of its release in the summer of 1999 and remember this. DVD and other releases do not have this scene. It was brief and might not matter much, but I was always curious why it was cut after the theatrical release.
Allegedly, there was a love scene between Theo and Nell which was removed to ensure a PG-13 rating. Portions of the footage have since been destroyed, although the soundtrack still exists. The scene was only 45 seconds long.
An alternate ending was allegedly filmed where Hugh Crane's ghost comes out of the fire place and attacks Nell.
There are some quick shots in the Making Of that actually didn't appear in the final cut. For example, when Theo and Nell wandered around the house, they found the corridor to the nursery room, to which Nell looks scared, and Theo rather indifferent. Also, in the scene where Luke is killed, Theo's reaction to it is longer.
Two little scenes are shortly longer in the DVD version of the film: After Nell arrives and is shown to her room, she goes to the window to look outside. The outside shot in the DVD is longer and the camera "climbs" a greater height. The other one is when Theo arrives, the camera walks with Nell for much longer than in the video version