The moments with L and Maki. Their big brother-little sister/father-daughter bond are just waiting to pull at your heart strings or waiting to make you throw up rainbows.
The moments with L and Near is pretty much the same.
The part where L mentions that Light was his first friend.
Light isn't even alive in this universe, and there is still plenty of fodder for shippers, starting with the way he wears Light's watch in "remembrance", strengthened by the quote "Light, it hurts... My heart-", and ending with his offering at Light's altar.
And also with Hideaki Suruga, L and Maki disguise themselves as a woman and young boy to get past some other FBI agents and L continually makes Suruga feel uncomfortable, calling him “honey”, winking at him, and otherwise coming off suggestively.
Moral Event Horizon: The members of Blue Ship (minus K because this happened before she joined the group) crossed it when they slaughtered a village full of people with a virus just to decrease the surplus population, believing that too many people in the world would destroy the environment.
"I will call you Near. Because you will always be near to those who need you."
Tear Jerker: Maki's stuffed bear being returned to her at the end.
Recording of Maki's Mom: Welcome home Maki. Did you have a good day? Maki: I had a good five days.
Recording of L: Welcome home Maki. Please have a good day tomorrow, too.
Maki: ...And the same to you, L.
The Woobie: L, Maki, and Near. Could even count as the Freudian Trio. L only has 23 days to live, Maki witnessed her father being killed, and Near just barely managed to survive bioterrorist attack in the village he once lived in.
