Many of the loading screens are recreations of NES and SNES game box art.
Contributed by ThisGuyInTheSuit
There is a cave called "From Cave" that holds many references to Demon's Souls.

•The cave itself is a reference to the company, From Software, who developed Demon's Souls. They also published 3D Dot Game Heroes in Japan.
•An item can be found inside called "Sticky White Stuff," which is a reference to the in-game item in Demon's Souls of the same name.
•Two messages can be found on the ground, one saying "It's safe here," and "I'm in trouble! Please recommend this message!" referring to the player-left messages.
•A "Hero's Soul" can be found lying on a corpse, just as in Demon's Souls.
•There is an NPC who says "Come on guys, this game isn't THAT hard..." referring to the overwhelmingly high difficulty of Demon's Souls.
Contributed by ThisGuyInTheSuit
If the player attacks a chicken enough times, a swarm of chickens will attack the player, just as they do in The Legend of Zelda: Ocarina of Time.
Contributed by ThisGuyInTheSuit