On Earthbound for the SNES: "If you own a pirated version of this game, beware. There is a chip in all legal versions of this game that is checked right before the final boss. If this chip is not detected, the game will immediately realize the game is pirated/hacked. This means that anybody playing a pirated version of the game will get to the final boss, then the game will freeze. The player will reset the game only to find that his file has been deleted. This has been seen as a "cruel" way to prevent pirating, but it made it impossible for anything other than a legitimate copy to be beaten."
More on the top videogame glitches here