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In "Another Day", Higashizawa uses the phrase "Dilly dally, shilly shally" to lure contestants into Molco. This is widely known as the exceedingly confusing phrase blurted out by Tifa to Cloud in Final Fantasy VII: Advent Children in an attempt to make him put his past behind him about being powerless to stop Aerith's death. Neku, rightly, is confused.
That would be in the English version only. The term used was "motto motto", which is like a motivational way to say "don't give up", "never give up", etc.
Strangely enough, The Wizard of Oz. The Game Masters and Kitaniji have the four cardinal directions in their names, and Neku and Beat both call Konishi a "witch" on a few occasions. The "nishi" in Konishi means "West"; as in the Wicked Witch of the West?
Darkstalkers. Uzuki's battle sprite has her holding her arms in a manner identical Morrigan's signature fighting stance, and her and Kariya's Fusion resembles Morrigan's usual Level 3 Super with Lilith.
There are several elements of the plot that seem to bear some similarities to Neon Genesis Evangelion, but it may be unintentional.
Marble Sentai Slashman is a phenomenon in the world of WEWY. Several NPCs are talking about it, and you can buy Slashman costumes in Another Day.