The best cube I've actually seen would be a Rubik's Cube. They're super cool, clever, and pretty. The only other non-fictional cube is the ice cube. I have only once seen ice cubes that were actually cubes, and they were a huge pain to get out of the ice cube tray. So, cubic ice cubes fail for being crappy, and non-cubic ice cubes fail for not being cubes.
My choice for fictional cubes is the Borg Cube. It is an iconic departure from typical spaceship designs in science fiction, in the same way that the Daleks were a departure from typical space monsters. The lack of overtly menacing characteristics makes it the more menacing, and its simplicity adds to a sense of foreboding mystery. I think it was a very clever and successful design choice. It narrowly beats the Companion Cube, which is similarly well-designed.