When playing as Raiden in the Plant chapter, go into strut C after the intermission sequence where Vamp kills the SEALS. Go into the women's bathroom, open a stall, then go into first person view. Look at the toilet. This might require several attempts. Call the colonel and he and Rose will be mad at you and Rose will not let you save the game. You can also go into the men's bathroom and call the colonel when looking at the urinal and he will excuse Rose.
When on the Plant chapter, after you get the Stinger Missiles find an area where there are seagulls . Lock on one of them and fire a missile. The colonel and Rose will call you on the Codec with a funny message.
While playing as Snake in the Tanker chapter, knock out an enemy then take a picture of him sleeping. This also works when you are being chased by the big heavy people with shotguns and take a picture of them. Onceyou have the picture and put them into the computer, Otacon will say that this is not a game.