Se-to-oh's name is a combination of Seto, a character from the Yu-Gi-Oh! series, and the series itself. He frequently references the series, even sacrificing monsters to summon a "Black-Eyes Blue Prinny", which is more than likely a parody of Seto's signature monster, The Blue-Eyes White Dragon.
Marjoly's "Omega Drain" and Dragon's "Dragon Flash" are both parodies of moves from Dragon Ball Z, Goku's "Spirit Bomb" and Piccolo's "Special Beam Cannon" respectively.
In the English localization, Mr. Champloo's speech pattern is a parody of celebrity chef Emeril Lagasse. Instead of saying "Bam" like Emeril, he says "Boom".