This is based on opinion. Please don't list it on a work's trope example list.
Tear Jerker / Children Of Eden
The expulsion, Abel's death, and the flood, natch.
Eve's monologue and the title song, "Children of Eden" at the end of Act I. Father finally speaks to her for the first time after The Fall. She sings a goodbye song to her large family, and her death is presented as walking up the staircase into Father's arms.
"The Hardest Part of Love"
Noah: That the hardest part of love,
Father: and the rarest part of love
Both: And the truest part of love... is letting go.
The reprise of the big love song then becomes about the entire family staying together:
In whatever time we have, for as long as we are living
We can face whatever comes, if we face it now as one
If there's silence in the sky, in a world without a future
We will swear to be together in whatever time we have.
The finale, In the Beginning.
That little reprise of 'Children of Eden' at the end of "In The Beginning" is almost too beautiful for me to actually listen to.
My choir sang this at my best friend's graduation (it was our fall show that year). It was particularly moving, with the parts of Japeth and Yonah sung by two graduating seniors ('This step is once again our fist/We set our feet upon a virgin land...") and the freshman chorus joining in at the last minute:
We cannot know what will occur
Just make our journey worth the taking...
"Stranger To The Rain" is heartbreaking.
I will dance before the lightning to music sacred and profane
Shed no tears for me, light no candle for my sake
The journey I am making now is one we all must make...
Close to Home. Adam and Eve have recovered from the expulsion and built a home and a family and are happy and it's all going to fall to pieces in the next scene. And young Cain and Abel are playing together
"A World Without You," where Adam is so deeply torn about whether to stay in the Garden with Father or go with Eve. He says that half his heart is his father's, half is his wife's, and all of it belongs to the garden. Father sounds genuinely distraught when Adam goes with Eve.