Camouflage
There is a wide variety of camo patterns you can wear in MGS3. Each one affects your "camo index" - a percentage displayed in the upper-right portion of your screen that determines how difficult it is for the enemy to spot you. It's common sense to wear camo that blends in with the environment.
Naked
Selecting this camo will remove the upper part of Snake's uniform. Only use this if you're confident in your sneaking skills (and have a lot of food - because your stamina will deplete faster while naked). No, there is no way to take off your pants, as Sigint will attest if you call him while wearing this.
Olive Drab
The most basic uniform, a solid green color. This is somewhat useful indoors, but there is little point elsewhere.
Leaf
Forest camo, designed to blend in with tall grass and bushes. You'll be using this a lot outdoors.
Tree Bark
This is more effective for lying down in dirt, or leaning against trees. You won't use this very often.
Black
Use this one to blend in with dark rooms, dirt, or just about any other shadow. Also works quite well indoors.
Tiger Stripe
Good all-around camo. Doesn't excel at anything in particular, though.
Tree Bark
Good when hiding against trees and logs, obviously, but also against dirt and rock.
Squares
Great in Rassvet and other brick areas, but elsewhere stands out too much.
Raindrop
Found in the alcove under the bridge in Dolinovodno. Occasionally it will rain, and this camo becomes very effective.
Choco Chip
Found in a tree stump in Bolshaya Past South. The brown-ish pattern of this outfit is best suited to desert or rocky areas (like the mountains). It also works somewhat decently against some buildings.
Splitter
Also found in Bolshaya past south, on a ledge. Good in buildings.
Snow
Take the right branch in the cave before fighting The Pain and keep going through the crawl spaces. Good in Rokovoj Bereg.
Special Camouflage
All of these camos have a special effect. Most of them are obtained by stamina killing bosses.
Animal
Obtained from Ocelot. Fur print pattern. Your gun will always stay perfectly steady when aiming in FPV.
Hornet Stripe
Obtained from The Pain. Leeches, bats, and spiders will not attack. Hornets will not affect you, and attack nearby enemies when you approach them.
Spider
Obtained from the Fear. Camo Index will never drop below 75%, but only when you have stamina left...and wearing it drains stamina fast.
Moss
Obtained from The End, by holding him up and threatening his head with your gun three times. When combined with Woodland and used in grass, your camo index skyrockets. Also, standing in the sun restores health and stamina.
Fire
Obtained from The Fury. Halves fire and explosive damage and gives immunity to burns.
Spirit
Obtained from The Sorrow, but you must reach the skeleton at the end of the river. It will be in your backpack when you get it from EVA. This one works particularly well indoors, and gives the added benefit of restoring your stamina when you choke enemies. Also dampens the sound of your footsteps.
Cold War
Obtained from Colonel Volgin in the Groznyj Grad hangar. Be quick about picking it up after he goes down; you have about 10 seconds before the cutscene. On the front is the USSR's flag; on the back is the USA's. The camouflage on this one is not that great, but more importantly, enemies looking at the Soviet side will hesitate to attack, sometimes not shooting at all.
Snake
Obtained from the final boss. Ostensibly gives great cover in every environment, but is it really that much work to change camos in each new area?
Sneaking Suit
On your second visit to Groznyj Grad, check the locker where you stashed Raikov (it has a red stripe and cannot be broken open). This is the best uniform in the game; it reduces stamina use, damage, and the chance of receiving serious wounds. Additionally, though it provides only about 10-15% camouflage, it ensures that your Camo Index never drops below that amount.
GA-KO
Found in Chyornyj Prud. When wearing this, enter and leave the Survival Viewer and the area's Kerotan will croak four times, helping you find him. Use in conjunction with the Directional Mic to aid your frog-hunting.
Banana
Get the best score on all the Snake vs. Monkey levels to unlock this permanently. Lousy camouflage, but makes all food taste great (like a banana, presumably?).
Fly
Kick down the last stall door in the bathroom on the second floor of the Graniny Gorki Lab. It supposedly makes guards hesitate to approach, but I never got it to work. Good for completists.
Disguises
You cannot use most of your weapons or items in disguise (save the cig-gas spray, hanky, and C3) but enemies will not immediately recognize you as an intruder if you wear a disguise.
Scientist
This is a Russian scientist uniform from the Graniny Gorki weapons lab. Use this to get around Graniny Gorki without alarming the guards (though the scientists will still run for alarm panels if you get too close to them). Press Triangle while wearing this to adjust your glasses.
Maintainance
This is the uniform the workers in the Groznyj Grad hangar wear, and is found in the second locker from the north in the easternost bank in the locker room. You can still plant C3 in this outfit, as long as nobody sees you.
Uniform
This is the uniform that you steal from Raikov in Groznyj Grad. Wear this in combination with the Mask (under Face Paint) to disguise yourself as Raikov and walk around Groznyj Grad without being spotted. Press Triangle while wearing this to salute (which the guards will respond to by saluting back). It has no effect during your return to Groznyj Grad (after the torture).
Tuxedo
Available at the start in a clear data file. You can use most weapons in this disguise (but not facepaint) but enemies won't be fooled for very long if you're seen. If you want to feel like James Bond, run through the game wearing this and using only the Patriot and silenced M1911A1. For a laugh, put it on after retrieving your backpack and call up The Boss...
Camouflage - Subsistence Only
These special camo patterns are only available if you're playing MGS3: Subsistence and you selected "I like MGS3" from the starting menu.
Desert Tiger
Like its name implies, this is a tiger-stripe outfit in a desert color scheme. It is also effective in wooded areas. As an added bonus, wearing this camo prevents attached suppressors from wearing out.
Flecktarn
This is a more advanced woodland camo, bringing your index up into the 90's - even if you're crawling in the open. However, it doesn't work too well in dirt, bark, or indoors. This camouflage prevents your battery from draining.
AUSCAM
This white camo is intended for use in alpine forests and such, and will make you stick out like a sore thumb if used in the jungle. To counteract being so obvious, wearing the AUSCAM reduces all damage to 2/3 normal.
Facepaint
The right camo pattern is only half of the equation. A bare face can be a dead giveaway, so it's important to conceal your face with a wide variety of different paints.
No Paint
Selecting this will remove the paint from your face. There's not much point to doing this, but it might add a bit of credibility if you're wearing the Scientist disguise.
Splitter
Looks cool and is effective in most areas, especially buildings.
Woodland
This paint works best in conjunction with the Leaf or Flecktarn outfits.
Black
Black face paint, obviously. Effective in the dark or against dark backgrounds, obviously.
Oyama
Found in the courtyard vent in Graniny Gorki Lab, this wacky camo makes Snake look like a geisha or Kabuki actress. Fun for screwing around and not much else.
Zombie
After defeating the Ocelot squad in Rassvet, look behind the barrels to the left of the exit for this facepaint. Not too useful for actual gameplay, but combine with the Spirit camo and you have yourself a pretty convincing zombie.
Desert
Found in the Krasnogorje mountains; very effective there and in other brown/tan areas.
Kabuki
After meeting EVA at the Tikhogornyj waterfall, go back out and look in the pond. Essentially, the male version of Oyama--no lipstick or rouge, but still a hideous, shrieking, "here-I-am-shoot-at-me" pale white.
Snow
Under a plank in a trench on the west side of Bolshaya Past Base. Good for the final battle in Rokovoj Bereg, but fails miserably elsewhere.
Water
After fighting the Fear, return to the entrance of Ponizovje South. It should be in the water (unsurprisingly). It's good if you need to swim past enemies.
Mask
Inexplicably, you start the game with this mask (and it's also shown in the introduction cutscene, if you selected "I like MGS2!" when starting the game). The mask looks a lot like Raiden from MGS2 (actually, it was designed after a Russian commander - Major Ivan Raidenovich Raikov). Wear this with Raikov's uniform to disguise yourself as him.
Facepaint - Subsistence Only
In MGS3: Substinence, selecting "I like MGS3" will start you with a whole slew of patriotic facepaints.
USA
Show your American pride as you empty your American-made XM16E1 into your foes, who saw you right away because you're wearing the tackiest damn facepaint there is! Seriously, it looks awesome but it's terrible at camouflage.
USSR
The Soviet flag. I never used it myself, but it might be helpful in red areas. Also, it might cause enemies to hesistate before shooting like with the Cold War camo, but I haven't confirmed that.
Germany
This facepaint looks just like the German flag.
Italy
This one looks like the Italian flag, and for some reason, also works well in wooded environments.
Not Quite Camouflage
Cardboard Boxes
Like every other Metal Gear game before it, the cardboard boxes make a complete return. You can use them to blend in with storage areas, or climb into trucks and convince the guards to drive you around Groznyj Grad (providing that the shipping address on them is correct). Just don't park yourself in the way of a patrol, or the guards will kick your box right off.
Monkey Mask
Unlocked by completing all the Snake VS Monkey missions. This doesn't really give you any tactical advantages, and as far as I know, it cannot be worn during cutscenes. It limits your field of view quite a bit. It does, however, amuse/confuse the final boss, which could give you a free shot.
Stealth
When equipped, your camo index skyrockets to 100% and stays there unless you touch an enemy or pick up a body.
