- How about just ten minutes into the film, with the scene of Ashitaka cutting his topknot off, as the Emishi elders lament what will happen to their tribe now that their last prince is leaving them forever.
- When Ashitaka is banished from his village ... and Kaya comes out against their customs to give him her crystal dagger so he won't forget her.
- Osa's speech. Just Osa's speech.
- San desperately clinging to the belief that she is a wolf whenever the differences between her and her brothers are emphasized.
- The scene where Ashitaka is too weak to eat by himself, so San chews the food up first and then gives it to him. Ashitaka actually begins tearing up at this display of unconditional care, it may be a factor...
- When "Mononoke Hime" plays for the first time, whether it's the Japanese or English version, the lyrics and notes will send you into chills and make you want to weep.
- Moro's guilt at having to leave her adopted daughter to assume her place as a guardian of the forest when her time passes. That this magnificent being feels such tenderness for a hairless human and even though she has given her a life that could have been ever tranquil and prosperous and could be still; Moro longs to give her adopted daughter everything she can't. She knows that the position she's put her in is untenable as San will not abandon her home even for love and a legacy of her own. So it is implied that for all the joy San has found as Princess of the Spirits; she is doomed to live forever until the forests fall. And for her tragedy to be eternal until the moment she rejoins the earth. Damn...
- San's backstory - her biological parents not only abandoned her, but sacrificed their own child to flee from Moro. The girl ending up as a beloved daughter of the very "monster" that was supposed to eat her and considering herself as a wolf makes it almost ironic, if it wasn't so depressive.
- Yakul getting wounded with an arrow. Ashitaka tells him to stay but the elk tries to continue. That's Undying Loyalty for you.
- Okkoto, limping away from the catastrophic loss against Jigo's men, confuses the skin-wearing people for his warriors and tries to lead them back into combat, only to be poisoned by them and become a senseless monster. His blind hope and desperation is terribly sad. What makes it worse is to see this once proud, albeit stubborn god be driven utterly insane.
- When San is knocked out by Jigo's hunters and trapped in Okkoto's demon flesh. Her groggy, terrified realisation of her plight as she wakes up along with the agony she's enduring as she tries to escape is just heart-wrenching. What's worse? It's outright stated that because of her resistance to the caustic qualities of demonic corruption; she would have also slowly become an avatar of hate and vengeance if Moro and Ashitaka had not saved her.
- Any time that "Adagio of Life and Death" plays. It's such a heartbreakingly beautiful track, that contains both sadness and hope - the scene where Moro and Okkoto die due to the Forest Spirit and Ashitaka races to save San is particularly poignant.
- This merits elaboration. When Okkoto, wreathed in the wrath of demonic tendrils, happens upon the Forest Spirit in his glen, all of the worms wither and die as his rage is immediately extinguished, and it even seems he can see again; though this is combined with an expression of fear so great that it almost qualifies him for woobie status. Then the Forest Spirit kisses his nose, and the mighty warrior's eyes drift closed, and he just collapses where he stands. Moro, weakly propped up nearby after having delivered San to Ashitaka, follows suit. The world had just lost two forces of nature like they were nothing.
- Moro's final act for San. She loves her "ugly, beautiful" daughter so much that she gives up her best chance at killing Eboshi to save her from Okkoto's demonic influence.
- The scene where the Kodama are all falling from the trees, fading out as they go. Peaceful creatures, having nothing to do with the wars around them, dropping like flies.
- When San stabs Ashitaka for saving Eboshi's life, he barely flinches, and even hugs her as the beheaded Forest Spirit is tearing up the forest.
- The fate of some of the residents of Iron Town. When the black ooze of the forest spirit washes over the town, they flee to the river. Some of them go the wrong way. You can briefly hear Toki scream "No, not that way!" just before they are instantly killed.
- The ending; between Joe Hisaishi's sublime score of "Ashitaka and San", the message that despite the fact that humans can be bastards and have serious flaws, there is always hope for them, and the last shot of a Kodama appearing in the ruined, yet rejuvenating forest, one line of dialogue is all it takes to kick it off:
"... I never knew the Forest God made the flowers grow."
- The person right behind Koroku . She was covered in bandages, and looks shocked at being all better. That woman was one of the lepers that Lady Eboshi took care of. Leprosy was a death sentence back then, and all of those gathered there were pretty much brought back from the dead.
- The film can be viewed as a Creation Myth for industrialisation: It's the moment where humanity, not understanding the damage it's causing, started taking more than nature had to give. Until then the forest had been able to hold its own but it had been weakening the whole time. And the natural world no longer has its gods to protect it. As San says, "The forest spirit is dead", and it won't be the same any-more. The death of the gods can be said to be the beginning of our climb into the present day world, and it's come at a terrible cost.
- What makes the film so profound is that hatred, love, ignorance and understanding are found on both sides of the conflict and that the Aesop of the film is not so much about environmentalism as it is about pacifism, tolerance and compassion.
- About six months after this film was released, animation director Yoshifumi Kondo died suddenly of an aortic aneurysm. It's sad knowing that this film was his last work as an animator.