Being a miserable obsessive nut that I am, I think I know all of them. Here's some pretty obscure ones I can come up at the top of my head:
1. In the Tanker, call Otacon repeatedly and he'll eventually talk about "a shadowy force" which unbeknownst to both of them at the time, were the Patriots. By starting a new game with a completed save data however, Snake will yell "LALILULELO!!!" if you hit the shoulder buttons, louder if you hit it harder.
2. Entering the Konami code in the VR Missions log in will unlock all missions.
3. Entering you DOB on your birthday will prompt a "Happy Birthday" message complete with a cake, which was not a lie at the time.
4. Talking to Pliskin about the M9 prior to his revelation that he is Snake will prompt him to comment on Solid Snake.
5. After meeting Stillman, go out to the CD Connecting Bridge, Snake is sneaking in a cardboard box. You can call him later and hear a humorous conversation between the two. If you destroy the box, Snake will remark that as well.
6. After being released in Arsenal, trigger an alert status, run back to the torture room and strap yourself back in. The Tengu will make comments.
7. There are multiple story branches in Snake Tales, depending on what you decide to do as Snake.
8. After defeating Vamp, there's a vent in the next area where you can spy on Emma, stare at her long enough and you'll get a call.
9. You can do an instant K.O by punching someone in the balls, but you can also do it form the sides and behind.
10. This is harder to pull off, but you have more kills, zero damage and performing way betterr than Snake during the Arsenal-Tengu team up, Snake will remark with a hint of jealousy. Thankfully they didn't team up in Rising.
Neat huh? Better be worth it since I typed all that myself!
Yeah, in the Codec screen. You have to respond at the exact moment Otacon utters "The Patriots". Hold down the button harder to get an even more exaggerated response.
As for the Arsenal section, it's much more difficult to pull off, but Snake will say something along the lines of "Why don't you worry about yourself!".
Here's another:
If you lie down on the swarm of lice during your arrival in Strut A, the sea lice will attach to Raiden's suit for the entire game, and even ending up as an inventory item while constantly eating up rations as time passes as well.
As far as I'm concerned, MGS2 had the most easter eggs of all the MGS games, closely followed by MGS3. I don't think there's that much in MGS4, nothing mind blowing anyway.
Great list, Ryan! . And duly, noted... I'll have to try all of these out .