Snake Eater Subsistence gets my vote. When you're good enough to creep through whole sections of the game without getting spotted like...
Slamming guards unconscious, choking guards out, tranquilizing guards, sticking up the guards, poisoning them with rotten food, using noise distractions (knocks and throwing empty magazine clips, hiding in cardboard boxes, distracting guards with dirty magazines, shooting down hornet nests and watching the insects chase them off... MGS1 was probably better in the story department but MGS3 (Subsistence) has the GOAT stealth gameplay IMO.
This is the GOAT walkthrough to any game...