There are a few times that I know of that there was a direct or indirect movie reference in the movies and the series that I have noticed. Now lets begin.
In the first movie; specifically after Littlefoot's Mother dies, there is a feeling that there is a Star Was reference in regard to Littlefoot's mother communicating with her son beyond the grave through objects.
In the second movie; after the gang take Chomper's egg and look after him, his parents come looking for their infant. To me this immediately reminds me of The Lost World: Jurassic Park for the same action, same response.
In the fifth movie; On the island where they made landfall, doesn't that remind you of the area in The Lost World: Jurassic Park where those cars and bus were parked?
In the episode: The Cave Of Many Voices; when Red Claw and his fast biters were in the cave and the gang were hiding in that cassavas, Chomper stated: "Don't move, Red Claw can't see you when you don't move." That is a modified quote from Jurassic Park when Dr. Allen Grant and Lex were staring face-to-face with the T. Rex and Grant said "Don't move, it can't see you if you don't move."
That's all I can think of right now, but if anyone else has any more, please free feel to reply.