Cubes are the easiest-to-find collectable in the game. They are obtained by either collecting 8 cube shards or finding an entire cube in certain rooms. There is a total of 32 cubes in the entire game, with most of the being collected by collecting cube shards.
Cube shards can typically be found in random places all around the game. Entire cubes can either be found at a dead end of one of the many directions you can go in the game, or as the reward for completing a puzzle, although it's more common to get an Anti-Cube as a reward to a puzzle.
You can technically get the 50% ending to the game with normal Cubes, but it's highly likely you'll end up getting a few Anti-Cubes in the process of doing so.