I enjoyed it for Ultima VII, where the manual was written as a holy book / biography of the main religious figure (antagonist) of the setting. You needed to answer questions from the book to be allowed out of the starting town.
King's Quest 5's copy protection (floppy version only) was enforced with a requirement to use a magic wand to cast a "spell" at various points in the game, where the "spell" is a series of letters that the player matches to symbols in the printed manual. Launching the boat was one of the points in the game where this was required.