Here is the full list of all 52 METAL GEAR SOLID 3: Snake Eater - Master Collection Version trophies - 40 bronze, 9 silver, 2 gold and 1 platinum.
Collect all trophies
Earn the title of FOXHOUND
Clear the game without entering Alert Mode (not including events where Alert Mode is mandatory)
Obtain the stealth camo
Obtain title of MARKHOR
Find all 64 Kerotans
Collect every type of medicinal plant
Find every type of camouflage
Find every type of face paint
Obtain the Infinity Face Paint
Finish game without killing anyone
Finish the game on any difficulty
Discover all first-person views that are not indicated by the button icon
Catch a glimpse of Ocelot, who’s seen behind the president when he tries to shake Snake’s hand
Defeat The Boss
Collect every type of snake
Defeat Shagohod
Defeat Volgin
Defeat The Sorrow
Use the Fake Death pill
Collect every type of weapon
Use a knife to remove a bullet
Defeat The Fury
Collect every type of bird
Achieve a camouflage index of 100%
Sneak up on The End and hold him up
Collect every type of mushroom
Catch a Tsuchinoko (mythical serpent)
Defeat The Fear
Defeat The End
Kill The End before the boss battle
Collect every type of fish
Defeat The Pain
Blow up a munitions shed with TNT
Collect every type of frog
Poison a guard
Create the Ocelot Time Paradox
Submit Ocelot
Use bees to harass an enemy
Collect every type of fruit
CQC Interrogate an enemy
CQC Slit an enemy's throat
CQC Slam a guard and knock him out
Hold up an enemy
Make Snake throw up
Call every Healing Radio frequency
Call one Healing Radio frequency
Eat a snake of any type
Capture any animal alive
Shoot a Kerotan for the first time
Achieve a camouflage index of +90%
Read all the pages in the Screenplay Book