Many of the character names in the game, such as Navarre, Isabeau and Aquilla are all references to the film Ladyhawke by Richard Donner

Walter's name is a reference to the Chaos aligned Hero nicknamed Waruo (translated as "bad guy") from the first Shin Megami Tensei. This is reinforced later [Spoilers] in Infernal Tokyo by Akira when he calls Walter a 'bad boy'.

The Black Samurai is wearing the armor from Shin Megami Tensei: Strange Journey.