While traveling with EVA, grab her, and interrogate her. She'll tell you a code that involves directions but then she'll say that she doesn't remember the rest of it. The code EVA was talking about was the famous 30 lives cheat code from Contra on the NES.
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.
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).
In the cave, bats attack you if you run. But if you use the active sonar and send out a 'ping', the bats will stop coming after you. That is because bats use sonar to see, they attack the strange noises snake is making and using the sonar tricks them into thinking you are just another bat.
When fighting The Fear, before you beat him, let him hit you a few times with his crossbow. The bolts will stay in your body, and you are supposed to remove them through the Cure menu. If you beat him, you will automatically be healed fully, but the bolts will still be stuck in you for the rest of the game. If you go to your Cure menu, you will see them sticking out of you, but you can't remove them. They are visible with any camo you wear, but not visible during cutscenes.
Defeat certain bosses by lowering their stamina to zero using the tranquillizer. This unlocks special camos that give you specific abiilites.