The entire scene when the girl Ayame recovers from her illness. Especially watching the fireworks afterwards. The game really lets you know that you've done something great.
Any moment when Chibi and his partners hug. Or whenever Chibi licks someone.
Manpuku reuniting with Charity. A lot of Manpuku's scenes are this actually. As a result, in the short time you have him around you'll grow to really, really like him.
This can also be a Crowning Moment Of Awesome near the end. To elaborate: Manpuku promised Chibi he would be there if he ever needed him, even if he has to violate space and time to help him.
Chibi and Shiranui meeting each other for the first time. No matter what, even when your heart is made of cold hard stone, it WILL melt once you see the two of them licking and stroking their heads against each other. The hearts only help show their family love.
On Kurow's deathbed, all of Chibi's partners and Isshaku tell him that he's not just a doll, he's his own person. Then, holographic pictures of his fond memories of his adventures with Chibi shine out of his amulet, reminding him that he led a good life. Doubles as a Tear Jerker.
In Ōkami, Susano had a picture of Kushi hidden behind a scroll in his home. Well, now that he's married to her, he doesn't really need to hide a picture of her now, does he? So whose picture does he replace it with? Why, Ammy's of course.