I could understand why you would feel sad about that scene. Even though I didn't like Frontier's second half, I thought that it had a pretty good finale. There also was another Digimon series, Savers/Data Squad, made and aired recently just to let you know.
There have been tons of tearjerking moments for me in various animated series and movies.
Land Before Time and Lion King-- I never could handle the scenes where the parents die and how their child responds without crying.
All Dogs Go to Heaven-- The ending with Charlie going to heaven always gets me.
Pokemon: I always cry after seeing Bye Bye Butterfree and Pikachu's Goodebye, which was also the first Pokemon episode I ever saw.
Digimon: The finale to both Adventure 01 and Tamers end in such a beautiful and sad way that I can't help but cry.
I'll think of some more later.