Rameses as he tries to appeal to Moses to stay with him. You can't help but feel sorry for him as he tries virtually everything to keep his brother from leaving Egypt, down to the sadness in his face when Moses does leave.
In fact, everyone in Moses' adopted family when he finds out where he came from. They are being completely sincere in their love for him, but the things they say to reassure him just drive him further away.
This part of the movie is devastating on Moses' end also. In literally less than 24 hours, he lost everything because he was unwilling to live a lie. The only thing he had left from his old life was the ring Rameses gave him, which represents their relationship (which makes it all the more sad when he has to give that up years later).
The short scene with Moses and Rameses after the final plague, ending with Moses breaking down and sobbing after. Listen closely to the ambient noise during this scene. Do you hear that almost inaudible screaming and crying in the background? That's the sound of thousands of Egyptians weeping and wailing over the deaths of their firstborn children. Also may double as Nightmare Fuel, if that kind of thing freaks you out.
"Deliver Us", especially the part Ofra Haza sang before the second chrous. This is even exaggerated by the Cantonese lyrics translated here:
My son, even I'm your mother, I have nothing to give
but just a glimmer of hope, that you may be on borrowed time
Hell, even the English lyrics are incredibly tearjerking:
My son, I have nothing left to give
But this chance that you may live, I'll pray we'll meet again
More heartbreaking in the fact that Yochaved never does meet her son again: she dies long before Moses comes back.
The plagues. It's so indescribably epic.
When Moses gives Rameses' ring back. It's the moment Rameses realizes that nothing can be the same among them again. The worst is how his face changes. From the deep sadness of a man who lost his brother, into the merciless, cold look of the Pharaoh.
Rameses wears the ring after that point, even during his last scene. Assuming he keeps wearing it, it will forever be a reminder of everything he has lost.
"Why can't things be the way they were before?"
After Rameses rejects Moses one final time ("And a great cry shall be heard in Egypt..."), Rameses's son looks at Moses, terrified. Moses looks back, and his expression makes it clear that he knows it's the last time he'll ever seen his nephew alive. Made even worse—Rameses's son is standing just below all the Hebrew babies, sent to drown, engraved on the wall. Made even worse if you think about how Moses went to talk to his brother and basically begged him to do what God wanted so nothing worse would happen (probably aware of what the last plague would be) and how he tried to stop Rameses from saying "And a great cry shall be heard in Egypt" (because in the end, there WAS a great cry and those words would haunt Rameses forever). Seeing Moses trying to stop his brother from saying this is awful, plus how he looks at his nephew, knowing there is nothing he can do now.
Moses: Something else is coming, something much worse than anything before! Please, let go of your contempt for life before it destroys everything you hold dear! Think of your son! Rameses: I do. You Hebrews have been nothing but trouble. My father had the right idea about how to deal with your people. Moses: Rameses! Rameses: And it's time I finished the job! Moses:Rameses! Rameses: And there shall be a great cry in all of Egypt, such as never has been or ever will be again! Moses: ... Rameses, you bring this upon yourself.
That brief moment of focus on Aaron and Miriam when the slavedriver Moses is about to kill first starts beating the old man. Miriam points the cruelty out to her brother, and he immediately turns away to work as intently as possible, with a terrified look on his face. And Aaron in general before the plagues. He's a man who has had his faith trampled into the dust, leaving only fear and bitterness. Listen to his voice when Miriam is about to charge at the guard. He's clearly begging her to not do anything to get herself killed.
When Moses inadvertently ends up near the house of Miriam and Aaron. The joy on Miriam's face as she is finally reunited with her brother dissolves into pure heartbreak when she realizes that he thinks of them as just another pair of slaves, especially when he raises his hand to strike her for her 'impudence'. Watch Aaron in the background during this scene. Near the end, just before Moses grabs Miriam's wrist, you can see Aaron shutting his eyes, bowing his head, and turning away. He doesn't want to watch because he knows his sister will probably be beaten.
The song "The Plagues" is epic as it is, but when you listen to the lyrics, it doubles as a heartbreaker, with Moses practically begging Ramses to free the slaves in order to stop the chaos.
Furthermore, this scene shows that Moses is just as emotionally tortured by the plagues as Ramses. After all, Egypt is his home... Well, was his home...
"This was my home
All this pain and devastation
How it tortures me inside
All the innocent who suffer
From your stubbornness and pride..."
While by this point Rameses is definitely in the wrong, he sings a short verse which has a quite sad passage.
"You who I call brother
How could you have come to hate me so?
Is this what you wanted?"
The aftermath of the Red Sea Crossing. First there's the moment before the Hebrews' rejoicing that they've finally managed to escape; there's an air of stunned shock and horror at the thought of how many men drowned when the seas closed... and then there's the moment when Moses looks back towards the distant shore, where Rameses is screaming his name, in an echo of when he left the first time. He sighs, mutters 'Goodbye, brother,' and leaves without looking back. Again.
In the opening song, Moses' mother prays she'll meet her son again someday as she sends him down the river. She never does- by the time Moses meets his biological family, she's dead. Worse, had she been alive when he came back, she would've seen a haughty prince instead, who would have thought her as nothing more as a foolish, deranged old woman who had the audacity to think herself his mother.
"The Queen's Reprise" of "All I Ever Wanted." So much love packed into so few lines. Contrasted with Moses' confusion and desperation, and with our knowledge of what's coming up, it's heartbreaking.
When the gods send you a blessing, you don't ask why it was sent.
Moses's nightmare involving him witnessing the Pharaoh sending soldiers to slaughter thousands of Hebrew babies, and after the Catapult Nightmare, Moses sees the carvings on the wall and realizes to his horror it's all true.