After your meeting with Granin, his door will become locked to you but you can still listen to him inside his office. After a few minutes he will start mumbling some curious things while half asleep.
In the office of Granin, there are models of things from other games Hideo Kojima Made. There is a model of Metal Gear Rex from Metal Gear Solid 1, A model of Metal Gear Ray from metal gear solid 2, and a model of Jehuty from Zone of the enders 1 and/or 2.
After being captured and waking up in the cell, throw back the food 3 times to see the scene where the soldier tells you his and his sons name (Johnny). Now wait a few minutes, Johnny will bend over, hold his stomach and will then run to the toilet. As a bonus, he will say some hilarious sentences like "Wow, that's a record!" or "Will that even flush?"
During the intro scene for Operation Snake Eater, you have the opportunity to press R1 to view part of the scene through Snake's view (the interior of the cockpit). When you do so, if you look all the way up (past all the instruments), you'll be able to see a poster of Yumi Kikuchi, a Japanese voice actress who had parts in Comic Party, Mahoromatic, Kakyuusei, and other shows.
After Volgin leaves the room after torturing you, Snake and Eva will be alone when the R1 button is prompted you can see some one behind with a board and a Codec number writen on it when your in the Cell call it and It will say "The door is open now".
In the fight with The Sorrow, go to your backpack and take out your camera and take pictures of all The Bosses, including Th Sorrow's Dead body, when you look at it, you will see the faces of the Game Developers.
At the end, when you do the quick draw with Ocelot. Pick the gun on the left, when you can shoot do not shoot at all. A hidden cutscene will happen with Ocelot talking about why you didn't shoot the gun.
When you are in the woods with Eva, shoot her with the tranquilizer gun. Walk right up to her while she is asleep (you may have to crouch). She will begin saying interesting things in her sleep.
In the Snake Eater Mission, go to compound area where the Hind sits. You'll know it's the right area because you'll see the Hind (Helicopter) grounded with noone piloting it. Interrogate the guard closest to the front door entrance of the largest building two or three times and he'll give you a password for Metal Gear Acid: V I P E R (Viper).
Its the guard you see on the second floor, when you first enter Groznyj Grad Weapons Lab: East Wing. Interrogate him to get the Acid... Password... X M E I G H T.
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