Kaya's parting words and her gift to Ashitaka on the eve of his banishment.
San tending to Moro's wound, without a single word we see how close the adoptive mother is with her chosen daughter.
Eboshi's kind acts. She buys the contracts of brothel girls so she can give them a home and place to work on their own terms. She also takes care of lepers and gives them work. The lepers and women fighting together to save Iron Town is also pretty heart-warming.
Whenever San's brothers, Ichi and Nii share a quiet moment with her, nuzzling into her hands so they can be petted both as a goodbye before her Suicide Mission and after when they are glad to see her return alive.
"Live. ... You're beautiful."
When one of the ape spirits makes a disparaging comment on how San isn't a wolf, her elder brother, Ichi, is so incensed on her behalf that he promises to break the chimp's neck for insulting his sister so.
The friendship between Ashitaka and Yakul. No matter what, whether it was being shot down or treading on sacred ground or even threatened with being eaten by wolves, Yakul always stuck by his master. He even tries to limp after him with an arrow through his thigh, and has to be ordered not to follow.
San taking off Yakul's reins and proclaiming him to be free is sweet in a misunderstood way; she just can't imagine any animal being in bondage and that only family would allow one another to be borne as a rider. Which of course, Yakul must consider his master to be so.
Yakul's little ruff shake to get rid of the itchiness after said harness is removed is also adorable.
San revealing that Yakul has told her of Ashitaka's home village and his people's respect for nature; all while scratching his chin, to which the antelope looks like he's enjoying the female attention greatly.
She then feeds a recovering and still weak Ashitaka as if he's a baby bird; definitely overlaps with Tear Jerker.
The Sleep Cute moment when Ashitaka wakes up in pain from his curse, to find San slumbering at his side, nestled in leaves and wrapped up snugly in her snowy fur wolf cape. He can't take his eyes off her.
When Moro describes San as her poor, hairless, lovely daughter. To Moro, humans are ugly precisely because of those reasons, but she looks at San with a mother's eyes. She may be without fur, fangs or tail, but she's her daughter, and that makes her beautiful. Also a massive Tear Jerker.
The way San cuddles up to Moro before heading into battle.
"That boy wanted to share his life with you..."
The Iron Town men, after being used as pawns by Jigo's monks to help dwindle the attacking boar offences, come to Ashitaka's aid in rescuing one of the wolves trapped under a dead boar. They even beat the amoral ass-holes over the head when they move to menace the young man from the east; then all pitch in to move the massive boar carcass.
Nii has just gotten free from being trapped underneath all the bodies of the boars and pretty much all the humans backed off after seeing him get loose, (though they don't attack either). We finally see that Ashitaka isn't the only human who knows how to reach out to others.
His faithful steed Yakul, despite being injured, hobbles over to the young wolf and they briefly and gently touch noses with each other, almost like saying "it's going to be all right".
Moro, despite having lost the use of her back legs, rips an unconscious San from the oozing mess that was Okkoto and gives her to Ashitaka, as if she knows that her daughter will be in good hands. The beautiful soundtrack only adds to the emotion.
After watching humans fighting against humans, humans against animals, and even animals against each other, seeing Ashitaka overcoming these barriers and befriending and making peace on all sides was both a Crowning Moment of AwesomeandHeartwarming.
The final scene when the Iron Town residents are out on the lake watching the mountain heal itself and plants return, and the lepers are cured of their illness.
The single Kodama appearing in the final shot. There is no going back to the way things were but there is still magic in the world.