Grand Theft Auto: San Andreas
Not all great manuals had to come from the dawn of time. Rockstar put a surprising amount of work into San Andreas' PC edition, with the game box remodelled into a tourist guide to Grand Theft Auto's fictional state. Where the guide began and the manual ended was often a blur, and for this reason it remains one of the few boxed PC titles still in my collection.
The Secret of Monkey Island
Not technically a manual, I know, but I couldn't let a discussion about them pass by without pointing out one of their siblings, the copy-protection device. While some older manuals were themselves a form of copy protection (games prompting you to enter words found on a certain page), Monkey Island went one better and included this code wheel, which was so great it was used again for the game's sequel.
Wing Commander 3
The game's manual wasn't the greatest, but the junk that came with it was. Included with Wing Commander 3 was a range of fictional reference material, like technical specifications for the game's starfighters and even an armed forces newsletter, complete with email addresses for those involved. For a game released in 1993, email addressed was a nice touch.
The manual. You cannot speak of instruction manuals for a video game without mentioning Falcon 4.0's, the colossus of the field. I mean, look at it. It's not a book, it's a tome, a collection of individual booklets giving you everything from detailed instructions on how to fly an F-16 down to the conditions you could expect to face in the game. When I first saw this, my mind could not grasp how heavy the game's box was with this inside it. Then, when I got home and after ten minutes couldn't even get my fighter off the ground, I realised it wasn't just big, it was necessary.