The end credits list the book "In the Darkness of Shadow Moses: The Unofficial Truth" (story in the "Special" section) as actually being written by Nastasha Romanenko.
The opening credits are made up of actual scenes from the game.
At the end of the credits, a conversation between Snake and Otacon reveals key information about the Patriots' Wisemen's Committee.
The end credits have several shots of New York, particularly Times Square.
During the opening credits, molecular diagrams appear, and from the atomic symbols on those diagrams, the cast's names appear. This is a reference to "Gattaca", which used a similar technique in the opening credits (and also shares a theme of genetic engineering).