Of course, this type of copy protection has disappeared now that everyone has access to the internet. Instead, we get Suckurom.
I remember the original Prince of Persia had a sequence based number or something (Page #, Line #, Word #). This code would give you a letter. (1 in 26 chance of being right). You had to enter a code every time you entered the game or levelled up. There were lots of chances to enter a letter.
I had an Indiana Jones game based on The Last Crusade on my good ol' Amiga back in the day. One of the levels was based on wandering around the tombs, but to enter the tombs you first had to enter a secret code, which you had to find in the manual. There was a long list of possible codes and you had to match it up with what was shown on screen. If you put in the right one, you could continue the game no problem - collect all your collectible bits, and eventually leave the tomb. If you put in the wrong code, you were sent to a 'dud' tomb that had no collectibles and no exit, and thus you essentially failed the game