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

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'.

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

After the Alignment Lock happens near the end of the game, if you return to Club Milton in Shibuya, you can view a hidden scene showing the accented club manager busily attending to a surge of demon customers. If you listen closely, the music that plays in the background is a remix of the Normal Battle theme from Shin Megami Tensei III: Nocturne. During the same scene, one of the sprites shown bears a striking resemblance to actor Heath Ledger, based on his appearance as the Joker wearing a nurse's outfit in the 2008 film "The Dark Knight".