Metal Gear Solid: Twin Snakes GameCube Eggs

Cameo: Alex from Eternal Darkness

Lay any book on the ground, then go into first person view. Look at the magazine and you will see Alexander Roivas from Eternal Darkness: Sanity's Requiem.

Cameo: GC and WaveBird controller

Go into Otacon's lab (where you fought the ninja), then go to the middle desk and look at the monitor. There you will see a Gamecube with a WaveBird controller next to it.

Cameo: Mario and Yoshi

In Otacons lab, you can find Mario and Yoshi figurines on top of a computer monitor. If you zoom in on Mario's head and shoot it, a 1-up message will appear over his head.

Creep Out Meryl:

Right before entering the room where you fight Psycho Mantis, stare at Meryl in first person mode and she will tell you that you are creeping her out and to stop doing that.

Developer Cameos

In the room where you fight Psycho Mantis, the portraits on the back wall are(left to right) cut-scene director Ryuhei Kitamura, Metal Gear Solid creator Hideo Kojima, and president of Silicon Knights, Denis Dyack.

Different Psyco Mantis sayings

Have either a Eternal Darkness, Legend of Zelda: The Wind Waker, Super Mario Sunshine, or Super Smash Bros. Melee save on the memory card you are using to save, and he will mention them before the boss fight.

Eternal Darkness Poster

In the armory room is a room full of nikita equipment. Inside is a locker. Open it up and there will be an Eternal Darkness poster inside.

Make Mei Ling Angry

If you call Mei Ling three times in a row and choose not to save, she'll yell at you for calling her for no reason. After this, she will stick her tongue out at you occasionally.

Also, right after you follow Meryl into the women's room, but before you trigger the cut scene, call Mei Ling and she'll yell at you for being a pervert, and won't let you save your game.

See Meryl's Underwear

When you first get to the Holding Cells area, and are going through the ventilation shafts to get to the DARPA Chief's cell, you will see a cutscene of Meryl in a prison cell, doing exercises. After the scene ends, you can look down into the cell to view her exercises anytime. If you go back out the cells the way you came in, and then come back to the vent above Meryl's cell, she will not have any pants on when you look down at her.

Snake's Haircut

In the 'Briefing' section in the title menu, watch every video available, including ones that are added to the list as you've watched more. Once you've seen every video (they will all have a check mark in the box next to them), choose 'Exit' from the list. You will then hear a hidden conversation that explains why Snake's haircut is different from how it appeared in Metal Gear Solid 2.

ZOE 2: The Second Runner Cameo

In the fight against the Ninja you can see a poster hanging from the back wall from Zone of Enders 2: The Second Runner.