Hmm...I wonder if we should make a list of the scenes we know (or can guess at) to be missing - this page just keeps on getting longer and longer.
Evidence Key:
S - Soundtrack
N - Novelisation
P - Promotional Stills
D - Director/Producer/Film Worker Insights
V - Video Footage From Film Trailers
*A longer version of the fight between Sharptooth and Momma Longneck - at least nineteen seconds worth of additional fight music appears on the soundtrack, yet we know the scene to be longer. (S, D)
*Possibly an extension of the "Berry Scene" - the soundtrack goes on fairly intensely for nine seconds. (S)
*A scene where the others find Spike sleeping after eating the plants surrounding his egg. Cera attempts to convince them to abandon him, but they ignore her. Ducky then lures him along with berries on a stick. (S? N? P)
*A scene where the GOF encounters an oasis inhabited by two rivalling factions of Dinosaurs, who refuse to share their food or water with one another, out of racism. Cera acknowledges such prejudice to be foolish. (N)
*Possibly an extension of the GOF eating the Green Food obtained from the tree. (P, V)
*The original ending scene - Littlefoot finding the Great Valley, leaping through the waters of the waterfall, then turning back to rescue the others from the Mountains That Burn. (S, N? P, D?)
*An extension of the scene in the lake, where they plan to kill Sharptooth to prevent him wreaking havoc in the Great Valley. (S, N)
*A short scene where Ducky makes faces at Sharptooth from the lake. (P, V)
*A brief scene where the others realise Petrie has survived the fall with Sharptooth, before all heading up towards the Great Valley. (S? P)
*A short scene taking place after the characters hug one another, where Littlefoot states “Now we’ll always be together.” (V)
Have I missed any? I wrote this from memory, and from briefly looking over the images of deleted segments that I’ve tracked down (mostly the ones listed here).
BTW, for sake of ease, here's the links again to the two video clips that I know of -someone linked to them further up the page.
LBT TrailerLBT Pizza Hutt CommercialHmm…does the bit at 0:08 happen in the movie? If not, that may be part of Littlefoot leading the others up to the valley!