In a meta sense, the fact that the film is honest from the start about its artistic license to the original text.
Many, but the whale shark scene is one of the first that comes to mind.
From the very first scene, the camera pulls back to reveal the stone head of pharaoh being pulled by hundreds of animated Hebrews. At that moment, you know this is going to be an Epic Movie.
The plagues is one for God. For once, He lets loose with His full power. And there is not a thing the Egyptians can do to stop Him. The highest point would be the scene where God kills all of the firstborns of Egypt— including Rameses' own son, which is finally what breaks Rameses and causes him to free the Hebrews.
A little digging into Egyptian beliefs brings out a new level to this. God isn't just using generic plagues to attack the Egyptians. He is mocking the Egyptian gods in the process, who tended to be patterned after animals, as well as the concept of Pharaoh being a god himself since this entire time he is powerless. Essentially, he is breaking the Egyptians by saying "See how your gods tremble before me?" in addition to suffering.
The entire burning bush scene, especially when God comforts Moses and says that he will smite Egypt with all My wonders. The music, the effects, everything about this scene gives me chills everytime.
And afterward when Moses runs back to Zipporah to tell her what happened. No dialog at all for a full 30 seconds, but the joy of one man telling of his experience of God is conveyed utterly and emotionally all in that wonderful music and the way Moses moves to tell the story of his new divine calling. That gives me the chills every time. Just Hans Zimmer's sweeping score and Moses telling what happened through gesture.
The parting of the Red Sea is a Moment of Awesome for both Moses and the animation studio.
And just before it, the Pillar of Fire. Which has the audacity to make its appearance by erupting up from underwater. It's just kind of awesome that after throwing all those natural disasters at the Egyptians, God's response to them still coming after His people to show his wrath in the most dramatic way possible.
While it's pretty scary, the entire sequence of the first 9 plagues, along with the amazing musical number, featuring a Dark Reprise of the song "All I Ever Wanted," is nothing more than awesome, even if it is one of the scariest things God has done since leveling Sodom and Gomorrah. The song itself is great, especially the lyrics, such as "I sent my scourge! I sent my sword! Thus sayeth the Lord!" The 10th plague though...
Pretty much every musical number doubles as this.
The entire When You Believe piece. It starts out as a single voice, joined by another, then a small group, until finally the entire nation is singing praises to their God for liberating them from slavery.