Awesome Music: The aforementioned song, Shelter, plays over the majority of the animation.
Heartwarming Moments: Many such moments, from Rin remembering her past interactions with her father to the man's decision to save her life and give her as happy a future as he could with the end of the world approaching. As well, Rin's reaffirmation that she's not alone as long as she remembers her father's love and thanking him for everything he's done.
Never Live It Down: The whole "Shelter is not Anime" debacle will be one incident that the Anime subreddit won't forget.
Tear Jerker: It's hard to find a moment in the animation that isn't this; everything from Rin having gone over 2500 days without any messages to the reveal that Earth was destroyed years ago and she's been kept alive physically (through a life support system aboard her craft) and mentally (through the technology onboard the ship that lets her create entire worlds to explore) in a spacecraft that her father made for her ever since.
Awesome Music: "Goin' Home," the song that plays at the end when Zach, Shaun, and and Cody happily plays together on the beach. Aside from being a catchy and suitable song to accompany the heartwarming moment, it nicely symbolizes how Zach is finally "going home" to what he really wants to do in life, happy at last.
Player Punch: The entire point of the game is making you care about your offspring, so it really stings when one dies. Shelter 2 has this trope even more so than the first game, because this time your young are kittens.
It's Short, So It Sucks!: One of the most common criticisms of both games. It's very possible to complete them within a hour or two.