Bathroom Problems:
When you're listening to the converasation between Ocelot and Solidus with your Directional Mic, press left to point the mic at the bathroom. You'll be able to listen to a very humorous scene where some guy is having problems on the toilet.

Daze the Guards:
Even the stealthy sometimes get caught. When this happens, a blue exclamation point will appear above the guard's head. If you shoot the blue punctuation mark, you'll knock the guard out temporarily.
 

Get Digital Camera:
After you beat the game, you can play the game over with the same save and you'll have the Digital Camera in your inventory for both the Plant and Tanker episodes. You can use this to take pictures and save them onto your memory card.
 

Getting Dog Tags:
Most of the normal guards in the game have Dog Tags that contain the names of the game's development team and those that won Konami's contest. To collect the Dog Tags you must hold up the guard and then make him shake and give it up by pointing your gun at his head or crotch. Dog Tags can be collected for each of the game's four difficulty levels.
 

Make Yourself Stronger:
Anytime you find yourself hanging from a bar or edge, you can press the R2 and L2 buttons to make the character do a pull-up. After you do 100 of them, your grip strength will be raised one level.
 

Skip Codec Text:
You can quickly skip through all the Codec voices and text by pressing the triangle button twice. The first will stop the voice and text and the second press will cause the rest of it to scroll through quickly.
 

Special Message From Otacon:
If you take pictures of all the girl posters, and the two locker doors that have a guy and girl on them next to each other, and upload them to Otacon instead of the photos of the Metal Gear Ray, you'll get some hilarious responses from him.

Waking up Soldiers:
If you need to get a Dog Tag from a knocked out guard, just spray coolant on his face to wake him up and then try to hold him up.
 

Zoom-in on Cut-Scenes:
Press the R1 button to zoom in on the real-time polygonal cut scenes. When holding the button down, you can move the camera around slightly with the right analog stick.

Get Digital Camera:
After you beat the game, you can play the game over with the same save and you'll have the Digital Camera in your inventory for both the Plant and Tanker episodes. You can use this to take pictures and save them onto your memory card:
 

Get the Wig:
First play through both the Tanker and Plant episodes and get every dog tag. Then start a new game and save. You will then have a wig in your inventory that gives you infinite ammo and allows you to not have to reload.

Reveal Cyborg Ninja:
When the Cyborg Ninja says "I'm like you, I have no name." QUICKLY press R1,L1,L2,R2 and his mask will flash on and off to reveal his face. Mystery! Big Spoiler. It really works!

9mm for Raiden:
As you start as Raiden look on the ground were you see alot of roaches.Not the roaches next to the wall the roaches on the ground next to the sewer crawl down and you will see a open sewer crawl into it and you will find a 9mm.

INFINITE AMMO:
Collect all DOG TAGS in the game, save then start a new game from that save game. Equip the WIG that you now have in the inventory.

SNAKE's TAG:
To get Snake's Tag you need to put him on sleep w/the tranqualizer and make him drop it. (NOTE. if you try to knock him out w/your kick-punch combo he'll kick your ass for sure)

Get Extreme Difficulty Setting:
Finish the game 1 time

Blue title Screen:
Finish the game 1 time