During Susie's nightmare during In Love And War, several cardboard boxes fall from the sky, some with the bottoms black, others white. Once they are finished falling, they resemble a giant checkerboard.
Doctor Who, "Mawdryn Undead": Turlough has an out-of-body experience following a car crash, and finds himself in a mysterious void with a checkered background, being recruited as a pawn in a Cosmic Chess Game.
The green tiles in Super Mario Galaxy and Super Mario Galaxy 2 will actually disappear if Mario/Luigi were to step on them. Also, in the first game, the staircase leading to the planet on which Mario/Luigi fights Bowser will be smashed apart by meteorites.
The Forest Temple has rooms with this pattern as well.
Sonic 3 & Knuckles features them quite prominently in the Blue Sphere special stages. Green Hill Zone doesn't count, however, since despite featuring a prominent checkerboard pattern, it's not actually otherworldly within the context of the series.
Touhou: In Fanworks, Sikieiki's Court has a chessboard floor, somewhat justified, given her ability to judge things black and white.
The Background in the final battle of Lotus Land Story uses a Blue and black checkerboard background.
Also the Palace of the Earth spirits has a Checkerboard floor
Yume Nikki has a checkered pattern on Madotsuki's shirt. The Fangames took that and carried on with it, ending up with this trope.
The Battlefield in Homestuck is a Checkerboard PLANET after prototyping enough times.
The world beyond the couch cushions in Ozy and Millie features a good amount of this. To quote the commentary in the book Prehistrionics: "My fondness for stripes, checkerboards, polka dots, arrows, and other pop-art-esque patterns has never been so obvious as it was during this storyline."
Due to the ease of generating a checkerboard pattern on an infinite plane, this is a common aspect of early computer-generated images. Compare the classic mirrored sphere on a checkerboard floor. Not to mention the famous checkerball from the early Amiga graphics demo (it was patterned so you could see that it was spinning) — so famous that it eventually became the platform's official logo.
Commonly used to represent transparency in images being edited. Used in Paint Shop Pro, Paint.NET, The Gimp, and others.