The No-Home Boys are a mashup of two popular series of young adult novels: The Hardy Boys (two boys solving mysteries) and the Boxcar Children (who travel the country having adventures).
First appearance of "The Kindergarten."
The bacteriophage/virus shaped crystal injectors foreshadow the story of the Gems on Earth.
In the kindergarten, Amethyst's quip to steven about the hole she emerged from is likely a reference to the short story "The Enigma of Amigara Fault" by Junji Ito.