I'm completely with you on that, Malte. I mentioned the discovery of the Great Valley, mainly because this post was made in the 1998 Theatrical Release forum, and to me, it was a powerful moment in the film.
For me, I found that two moments in LBT 8,
1) When Spike first arrived at the hot spring with his herd, and the Gang saw him again for the first time
2) When Spike's "mother" rescued Spike from the ice; "Of course I did; He's my boy!"
were very emotional.
Another very powerful moment to me, is near the ending of LBT 10, which is why I enjoy the film as a whole, and the song "Bestest Friends" so much. The thought of the number of experiences the gang has had, and the attachment they have for each other, is truly brought out in this song, and this moment in the movie. The first time I watched it especially, when I didn't know exactly how Littlefoot would respond to the decision that was to be made, made it a Very emotional ending to the movie. His Grandparents were overjoyed to see Littlefoot returning home with them; the Gang could stay together (if Universal really wanted to, they could have ended the series right there, with Littlefoot leaving. I'm very thankful they didn't take that route out, for a number of reasons), and we got to see the true closeness the Gang has to each other, and to Littlefoot.
To me, this is the essence of the series (friendship, overcoming challenges against all odds, and on some level, love), and these moments showed those elements in detail, which are among my favorite moments in the LBT series.
Also included, are all those that Malte mentioned (Ali leaving in LBT 4, Mo Leaving in LBT 9), though for Whatever reason, I couldn't get As attached to Chomper. I didn't get the same impact when Chomper left after LBT 2.
What did get me though, was the joy when the Gang was Finally with their families again, at the end of LBT 5. That is another moment I very much enjoyed.
I'm in full agreement with you, again, Malte, that the music does indeed play an important role in the emotional effects of a scene. Even the song "Bestest Friends" (I know I'm referring to this song a lot. As you can tell, I like it

) has some highly emotional elements. The first time I heard Cera sing her solo lines in the song, I just thought it was beautiful to see this side of her. I knew she had it in her, but it is shown so rarely anymore.
"...No matter where you are..."
"...I'll see you in my dreams..."
Gorgeous song, and A Very good ending to a flawed, yet still entertaining film; LBT 10.