The US Official Playstation Magazine pointed this out in their E3 2003 Issue.

At E3 2003, (the game festival), at the Metal Gear Solid 3: Snake Eater booth, they were handing out brochures. On the back panel there are a bunch of letters scattered all over the place. Some are white, some are gray, and some are a darker shade of gray. If you were to look, the darker gray letter that's closest to the top of the page is B. The next darker gray letter closest to the top of the page is I. Then come G, B, O, S, and S. This gives you B-I-G-B-O-S-S, which spells out "Big Boss." This is a secret message from Hideo Kojima, the game's creator.