I read that in Batman AA the developers made it so that if you were playing a copied game batman was programmed so that he didnt know how to use his cape correctly. This made the game almost unplayable as at a certain point in the game you had to use the
cape to glide to safety.
Best one was an old anti piracy measure an amiga game had. It was some space shuttle simulator but if you failed the anti piracy check the game made you go through the full three days of pre flight checks in real time with no way of speeding up the process.
On topic though , i think the ones at the start menu for Back Ops were clever , the pulling of the triggers to bust outta the chair and then typing stuff into the comp terminal to unlock the random stuff.