Its surprising how many there are for me:
II: Littlefoot and Chomper saying goodbye. It wasn't particularly sad, but definitely was the closest thing. Emotional, well performed, and with the perfect soundtrack.
V: Always There- First LBT moment to genuinely make me cry since Littlefoot's Mother in the original. Mostly quite sad, topped off by Littlefoot's solo. because you think it would be about his grandparents, and then it sort of hits you that he's referring to his mother for the first time since the original.
VI: When You're On Your Own always gets to me a bit, especially the "When you're on your own/ you have be the grown-up" bit. Just the sudden change in mood, from thinking that being on his own was exciting and adventurous, to thinking that it's lonely and harsh. Particularly because being a bit of a loner makes me think such things sometimes.
VIII: Contrary to what many people say, it's not the Family song. It's the little dialogue-less montage of Spike and Ducky slowly growing apart. I dunno why, but speechless montages always get to me in films. Personally, I blame the first 15 minutes of UP.
IX: No One has To be Alone. Oh man, this song always gets to me. Just the opening, with Mo and Littlefoot quietly enjoying a moment, and Littlefoot realising the meaning behind his grandpa's words. Plus, I dunno why, but the "There is so much more to everything/ than we can ever know" bit always gives me a big shiver, which I take as a sign of power and atmosphere in a song.
X: That brief shot of Littlefoot brooding on the ledge before Bron talks to him. The combination of the image of Littlefoot possibly sadder than he's been since the original, plus the twinkly Ghibli-style piano music. Part of me wants this shot to be longer, while the other half reminds me that this could cause Littlefoot to look angsty.
Also, the Bestest Friends song. Like LBTfan said, if I didn't know that there were 3 more sequels, I would be very emotional and into this scene.
Also, that brief shot of Petrie apparently being swallowed by the belly-dragger. Not exactly sad, but first time I saw it, I got a real "......oh my god!" reaction from it.