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.
Their gods don't just tremble; they flee. He has full authority and power, and the various Egyptian gods can't do a damn thing to stop Him. Here's a brief breakdown of how every single prodigy before the Exodus hit Egyptian beliefs and their very way of life:
the staff-to-cobra transformation caused such a panic because it's a symbol of two goddesses: Meretseger, the guardian of the royal tombs, and, most importantly, Wadjet, the symbol of the royal power of life and death (hence why the pharaohs and a few other members of the royal family wore a stylised cobra on their heads). That's also why Hotep and Huy could pull it: they are the court mages, playing with cobras is part of their job. Not only that, but Moses' staff-turned-snake manages to consume the other two cobras whole;
the Second Plague, the frogs overrunning Egypt, continues the mockery of a good omen: the frog is a symbol of fertility and the god Hapy, a personification of the flooding of the Nile and its fertile silt, and smaller 'invasions' of frogs would come right after the flooding;
the Third and Fourth Plagues, the mosquitoes and the fleas, are a direct consequence of the end of the Second: there were no frogs to eat them anymore. What's worse, the Egyptians were used to dealing with them, but this time there were too many;
the Fifth Plague, the disease of the livestock, hits a soft point of the Egyptian believes: the cult of Apis, intermediary between men and gods, with a living incarnation as a bull (the Egyptians also built graves for these bulls). Because now Moses is the intermediary, Apis dies, and no other bull with the proper markings shall be found;
the Sixth Plague, the boils, hits particularly hard: boils and other illnesses fall under the dominion of Thoth, the God of Science and Knowledge, Medicine and, what's worse, the Arbitrator of the Gods, who would bring justice and properly administer the law. Between the epidemics and the priests having no knowledge on how to cure this, this one is a warning that Egypt has brought itself outside of the law of Maat, its greatest moral value;
the Seventh Plague, the storm of fire, is personal for the Pharaoh and the royal family: storms are the dominion of Seth. In this time not only Seth is not yet demonized (that would happen only from the Twenty-First dynasty, and the names of the Pharaohs indicate the Nineteenth), but it's one of the most important gods, with Rameses's own father being named after him and the current capital of Pi-Ramses (cited by name in the Bible as the starting point of the Exodus) is a center of Seth's worship. Ouch...;
the Eight Plague, the locusts, is pure nightmare: while in small numbers they were considered symbols of luck alongside grasshoppers, in large numbers they were rightly feared, and by being brought by the wind this plague entered the dominion of one of the most important gods, Amon;
the Ninth Plague the Darkness, is again personal with the Pharaoh and his family: not only the authority of the Pharaoh is associated with the Sun God Ra and the Sky God Horus, but the reigning Pharaoh is Rameses, meaning "Born from Ra". A message of paternal and divine rejection?;
the Tenth Plague is linked to a specific Egyptian myth, the Eye of Ra. In that myth, the men had disrespected Ra and planned to rebel and kill him, so he sent his Eye (identified with either the war goddess Sekhmet or the gentle HathorDepending on the Version) to punish them with a slaughter... And in one day she killed half of mankind, all the guilty and many innocents, and to stop her finishing the job the gods had to get her drunk. The message here is: "Let My people go, for if you continue to sin all of Egypt shall die in a heartbeat". No wonder Rameses finally relented...
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.
Ramses gets one in this scene as well. This is the same God that has devastated his people, destroyed his empire and killed his son. And now this god is directly attacking him with a pillar of flame. How does Ramses respond? By trying to outmaneuver Him by running around the fire wall.
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 saith 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.
In spite of it brimming with arrogance, and being the closest thing the movie has to a Villain Song, Playing With The Big Boys Now is a very impressive musical number, whether its the truly intimidating backing track that combines darkly building chords with the names of the Egyptian pantheon, or the admittedly impressive showmanship of Hotep and Huy.
The animation in this movie is flawless, not just in its appearance but in it's implementation, with every scene being framed perfectly. The direction of this movie is masterful.
Speaking of the animation, there are several moments where there is Conspicuous CG included in parts of the film, including the chariot scene, several of the plagues, and even the Burning Bush. Both first-time and hardcore viewers don't notice this unless they view the Behind the Scenes for the film. Yes, Dreamworks combined both 3D and 2D animation into their film and successfully pulled it off.
Tzipporah openly biting the hand of a prince of Egypt! Why is this badass? Because she probably knew that doing so could get her beaten or killed, but she does anyway because she's a woman who won't take crap from anyone! Including a prince.
Then, how she was able to escape with no one detecting her (except Moses).
When Moses looked like he was going to be injured by Ramses's armed guards, Tzipporah immediately moved to stop them (or at least try to get Moses out of the situation). Aaron stopped her for a few seconds to keep her from getting hurt, but she broke free quickly and continued to run. However, the first plague (turning the river into blood) stopped any violence from occurring at that time.
Can we talk about Miriam for a second? She is awesome personified. I mean, she is a Hebrew slave, somebody with zero power or agency. Yet she is able to channel the only resource she has — her faith (and not just the spiritual kind) — and uses it not only to rise above the despair of her own situation, but she also uses it to push her brother into liberating an entire people. She constantly lifts everyone else's spirits, no matter how badly they treat her. She is Moses' first supporter, the only one who has never doubted him or his mission, and often it seems her unshakeable belief in her brother is what keeps Moses from giving up. No wonder he pulled her aside and thanked her at the end of the movie.
And she does it all without being fanservice or somebody's love interest. Which is pretty rare for an animated heroine.
A small moment that is still a nice touch from the animators; when God, through Moses, turns the Nile to blood, the whole river runs red...except for a small clear circle right where Moses is standing.
Yocheved. Just Yocheved. While she didn't have a major crowning moment, her Mama Bear instinct to save her youngest child (Moses) from death is not only beautifully heartwarming, but pure awesome.
Another moment from the burning bush scene is when Moses repeatedly questions God and doubts that he can do what He wants. God decides to persuade him via a Badass Boast.
God: WHO MADE MAN'S MOUTH?! WHO MADE THE DEAF, THE MUTE, THE SEEING, OR THE BLIND? DID NOT I?! NOW GO.
In a meta sense, the fact that the film is honest from the start about its artistic license to the original text.
While at the same time they tell you that they really did their research; interviewing dozens of religious scholars from three different faith groups in order to portray the events as best as possible.
The result is so accurate, and so respectful, that the movie is widely regarded as a better representation of the story than The Ten Commandments.