In the downloadable content The World of Recycled Vessel (15 Nightmares), two sets of costues can be unlocked by completing doors 1 and 2. You can activate the costumes in the options menu in the title screen of the game.
Both costume sets alter the appearance of Nier, Kainé, Emil during gameplay and non-cgi cutscenes. They'll also replace Yonah during the loading screen with Kainé and Emil respectively. Further, both change the skin of magic orbs, shot by enemies, to Emil's face.