There's something rather sweet about how despite wanting to wither the whole forest, Even Evil Has Loved Ones, and the villain and his son actually have a good relationship before the son's death.
In nearly every single scene he's in, Mandrake is either talking to or talking about his son. It's very clear how much he means to him.
Ronin allowing Grub to become a Leaf Man.
Going against the Leafmen's, and the order of nature's, code for never revealing themselves to humans, the end shows that MK, even after transforming back to her normal size, keeps in touch with Nod and her miniature friends through her father's cameras akin to Skype.
In the Creative Closing Credits, at the 'production babies' section, there's a picture that MK drew of her complete family (her, her father, her mother, Ozzie) when she was a little girl. Also counts as a Tear Jerker.
Early in the movie, MK states she's going through the Five Stages of Grief over her mother and she intends to do it alone, to the disappointment of her also mourning father. However at the end of the movie when MK grows big again, it's hinted that she's willing to let them get through the grief together.
Right after MK is shrunk, she's obviously terrified and confused, but still is primarily concerned with the wounded woman in front of her. In fact, when the Leafmen first arrive, MK clearly has no clue who they are and what their relation to the Queen is, and her first instinct is to try and shield Tara with her body from what might be a threat, even though she's just a scrawny teenager and these people are clearly battle-ready. She doesn't let go until Ronin calls the woman in question by name and gently takes her in his own arms, because that convinces her that they won't hurt her. This girl just had something handed to her that she doesn't understand, but she immediately tries to care for and protect a woman who is a complete stranger, even though there'd be no way she could succeed.
Finn's interaction with Ronin after Tara's death. It's clear that Finn is very concerned with how the general is handling it, and wants to make it better.
Ronin: Take the Leafmen to Moonhaven; fortify it. Keep everyone safe.
Finn: What about you?
Ronin: [Beat] Mandrake will be looking for this pod, but he won't be looking for a Leafman traveling alone.
Finn: That's not what I meant.
Ronin: (lays his hand on Finn's shoulder) I know what you meant.
Nod and Mk's deer ride.
Ronin laughing at, and joining in with Nod mocking Bomba. It's nice to see him smiling and laughing after what happens earlier on.
When the Marigold Girl is chosen as the next queen, Tara's ghost appears kneeling in front of her, giving her a simple, but rather sweet final wish.
Tara: Look after them for me... (Looks at Ronin, who's clearly smiling) There's that smile...
The main protagonist is named in honor of Joyce's late daughter, Mary Katherine. Made more poignant in that the real-life MK was around the character's age when she died.