As with the main page, all spoilers below are unmarked
Super Smash Bros. Brawl is referenced directly in some of the tutorials and a random dialogue when Pit is using a bow:
Palutena: It's a pretty well-balanced weapon. Pit: Yeah, I used one in the last brawl. Palutena: Brawl? How horrible! Were you hurt!? Pit: No, it was a smash! Palutena: I just can't picture you in a melee. Pit: That's because I wasn't...
The Komayto enemies are based on Metroids.
The idol description for them references the opening of Super Metroid.
"The last Komayto is not in captivity and Skyland is not at peace."
A dialogue between Pit and Viridi directly references the Metroid franchise.
Pyrrhon mentions reading up on the Aurum on Divinipedia.
The Hedgehog Claws' idol mentions that the weapon's main characteristic is the large speed boost it provides to its user, referencing the main ability of Sonic the Hedgehog.
In the game, there's an enemy called "Collin" that can only be killed when you hit back the enemy it fires. The idol for this enemy says the name of the fired enemy is "Phil", and the idol is named "Collin and Phil". Flip the two names around...
While Pit is talking about clubs with Viridi, he says, "Talk softly and carry a big stick!", a phrase coined by Theodore Roosevelt.
During the tutorial, Pit asks if Palutena will be sending him a machine-gun-toting robot girlfriend, a reference to Curly Brace from Cave Story.
In the Chaos Vortex level, Hynden Walch (voice of Viridi) starts slipping in and out of her Princess Bubblegum voice. At first, it's rather subtle, with her at one point calling Pit a "dingle brain" in Bubblegum's style of speaking. Then, later in the level, she says, word for word, and in the same style of the Adventure Time promos, "What time is it?"
Danny Mann, the English voice actor for Thanatos, is very clearly doing his best Ed Wynn impersonation.