Snake Eater for sure. A true master peice in gameplay, boss fights, and story. MGS4 while epic, didn't really feel like Metal Gear Solid in a few ways; No new version of Metal Gear (No, Gekko's aren't Metal Gears), all other MGS' hae you infiltrating a base of some sort. MGS4 on the other hand took you all across the globes for a relevtivly short amount of time.
EDIT: Oh yeah, the addition of Drebin/black market purchasing most types of weapons, ammo, and items at any given point in time REALLY broke the OSP system I loved so much. Unless Metal Gear Raiden or whatever its gunna be called is a Devil May Cry try of game, it should've been put in that instead of MGS4... just my opinion though.