When using the "Fist" sub-weapon, Juste will yell out "Oraoraora!!". This is likely a reference to JoJo's Bizarre Adventure, and the main character Jotarou Kujo, Star Platinum, repeating "Oraoraora!!" over and over again while punching.
The wind and bible Spell Fusion will give you a shield, a reference to Konami's Gradius series.
In the Den of Skeletons, in the background you can find skeletons of the bosses Slogra and Gaibon, both from Super Castlevania IV and Symphony of the Night.
In one of the rooms found in the Den of Skeletons, a statue is visible in the background. This statue heavily resembles Dracula's final form in Castlevania III.
There is a monster you fight called the Simon Wraith, as it mimicked the protagonist Simon from the original Castlevania. In Japanese, it was called Shimon, which is how you write Simon in that language. The kanji literally meant "Gates of Death".
You can find a giant skull with several holes in it, used as a ramp. This is a reference to the mini-boss "Crocomire" from Super Metroid. It's thought to be a way of paying tribute to the Metroid series, as Super Metroid heavily influenced the Castlevania franchise. A Crocomire reference also appears in Donkey Kong Country Returns.