In order to cover up the character Raiden, the promotional trailers for the game showed several scenes with Solid Snake in different scenes. In the final game, Raiden is involved in the same scenes, but in Snake's place. Hideo Kojima used computer tricks to cover up Raiden and no one knew of his existence until the game was released.
Snake's alias, Pliskin, comes from Kurt Russell's character, Snake Plissken, in Escape from New York (1981) and Escape from L.A. (1996).
Some of the exchanges of dialogue between Jack and Rose are based on those between Hideo Kojima and his wife. For example, before they got married, she would always ask him what day it was. Once, when they had a date, he completely forgot about it. This is what Rose's continuous asking Jack "what day tomorrow is" is taken from.
During the conversation between Snake and Raiden in Arsenal Gear, Snake points at his bandana and says, "Infinite ammo." This is a reference to the first Metal Gear Solid, where you received a bandana if you managed to complete the game with Meryl still alive.