It should be noted that for older viewers, it would have simply made the film better. Which is why fans are trying desperately to track down these scenes.
What Could Have Been: The film's second half was not as Don originally intended. In the original version, Littlefoot finds the Great Valley after he goes off alone and the others go with Cera. He realizes that he has to go find the others, because they won't find it on their own, and goes back after them. The Sharptooth scene then happens and he leads them to the valley. This can be detected in the final film. Look at the scene where Littlefoot is telling his mother he'll never find the great valley because it's too hard. The rock they pushed onto Sharptooth is still there in the background.
There is also a deleted scene where the group finds an oasis, but the two groups of dinosaurs already there get discriminatory, and say that only Ducky can drink.
These elements still appear in the children's books released with the film.
Other things changes include: The scene where Sharptooth lands on the back of Littlefoot's mother was originally fully visible, but it was changed to shadow. The scene where Sharptooth is pushed under by the big rock had a scene where Sharptooth was seen looking up to the water, but it was also deemed too scary. Fans have gone out of their way to find all these scenes. Hopefully they'll be found in the future...
Old Rooter didn't appear in the original script, but was added to soften the blow of the death of Littlefoot's mother.
The original film trailer has another apparently deleted bit from the final scene with Ducky saying "now we'll always be together!".
Reportedly the full, uncut version has aired in several foreign countries.