Tanker Mission/Solid Snake
These can only be done on the Tanker chapter, or when playing as Solid Snake (whether during the Tanker mission, VR missions, or Snake Tales missions).
Otacon's Savegame Proverbs
When you save the game (140.96), Otacon will read you a Chinese proverb, much like Mei Ling did in MGS1. However, for each time he does this, he gets worse at interpreting them, and the "meanings" to each proverb get more hilarious each time, as does Snake's response to them. Note that you may have to switch between areas a few times before Otacon will read another proverb.
The Locker Incident
Think back to when you first met Otacon. He was in a locker, right? Well, hide yourself in a locker and call Otacon. Snake will reminisce about the good old days, and get a cheap shot at Otacon while he's at it.
Raven
You encounter an action figure of Vulcan Raven in the engine room, situated in front of a flashlight. Shooting him will knock him over and make him start firing BB rounds all over the place, making angry noises in the process.
Any Codec Moments From You, Snake?
Much fun can be had with Otacon's digital camera. From the very start of the game, you can take pictures of pretty much anything. You've only got around five slots to save the pictures, though, so make them count. Take a picture of the girly poster in the locker room on the lower deck. Take more pictures of the girly posters you encounter throughout the ship, especially the ugly girl in the engine room, and make sure to include at least one shot of a guy poster (the muscleman poster nearby the Raven action figure works best). Finally, if you're fast enough in getting to the cargo holds, some of the marines will be in their underwear. Take one picture of a pants-less soldier and then submit your lot to Otacon before you take any of the Metal Gear photos.
Plant Mission/Raiden
These can only be performed on the Plant chapter, or as Raiden.
Where Am I?
When you're on Arsenal Gear (preferably while Raiden is still naked), repeatedly go between the torture room and the jejunum area. Eventually the location names on the loading screens will start to get a little strange.
Poor, Tired Emma
Shoot Emma with a tranquilizer dart. She will eventually start mumbling in her sleep.
Fortune Smiles Upon Thee, Parrot
The parrot that you find in a computer room seems to mimic more than just speech - try shooting at it with any conventional weapon, and your bullets will magically curve around its cage, much like Fortune!
You Must Be Ames
Take the directional microphone out when standing next to Emma's parrot and repeatedly press Triangle to call for Ames. At some point the parrot will start repeating, "You must be Ames!"
Johnny Sasaki Remix
Johnny Sasaki, the now-legendary Diarrhea Guard from MGS1, makes a comeback appearance during the scene with Olga, Ocelot and Solidus in the meeting room. Point the directional microphone off to the left side of the room, and you'll start hearing a very different event going on.