The treatment of the baby Ohmu gets this devout insect-lover wibbling like crazy. The humans capture it, spear it all over, and drag it through the air, squealing pathetically and bleeding, as bait to draw out the parents, because Humans Are Bastards. Sure, everything turns out okay in the end, but the moment is definitely there.
When Nausicaa tries to keep the baby Ohm from moving and her foot hits the acid lake ... lets just say that it is hard to forget her heroic pleading screams. Pass the tissue please.
Another thing to remember is that Nausicaa's foot was injured, because she'd been shot. So some of the acid got inside the wound...
Teto's death and burial in the manga.
Also in the manga, Lord Yupa sacrificing himself to protect Kushana. He smothers a grenade in his cloak, and even though he doesn't flinch when it blows his arm off, at that moment you realize he's a goner.
Nausicaš talking to Lord Yupa in her plant chamber about how she discovered that it isn't the plants of the Fukai that are poisonous, it's the soil they grow from. She then goes on to say that she was experimenting on ways to nurse her father back to health, but due to him getting assassinated it's all been in vain, and seeing as there is no point in continuing her experiments, she has shut off the water supply. She explains all of this very calmly, but then breaks down in Yupa's arms.
Lastelle's death at the beginning. Nausicaa does everything in her power to save this girl she barely knows, but once she catches sight of the wound in Lastelle's chest, she knows there's nothing to do but let her die in peace.
Ohma's death in the manga. "I'm unsure, mother. Have I become a good person?"