After defeating Screaming Mantis and immediately after Psycho Mantis vibrates your controller, keep pressing X to see Hideo Kojima.

If you prolong the Psycho Mantis fight long enough, the game will show the opening screen, except the word "Kojima" will replace "Konami". The game will then resume the Psycho Mantis fight.

Press L1 to examine the .50 Cal Anti-Material Sniper Rifle to see "Recommended by Hideo Kojima."

When Snake hides from the two Irvings next to the box of watermelons, the box reads "No Place For Hideo."

You can see a ghost image of Hideo Kojima in Otacon's lab using the camera. It is between Policenauts and the poster that from a distance reads "Final Fantasy VI".