Metal Gear Solid: The Twin Snakes ranks number one for me; the original story with updated control scheme and graphics is awesome. Then it’s a toss up between 2 and V. 2 is a solid game in the same mould as the first, but V allows me to Fulton extract unsuspecting enemies which is a genius mechanic that allows me an immense range of fuckery.
To be fair, your username kind of suggests you want to look inside everything anyway