Well to me all the games were legendary so i dont know. It might be twin snakes for i adore foxhound & the boss batlles were creative, also Gray Fox is awesome, & just the whole story of the first one in general was awesome.
Now metal gear solid 3, this game i like no other, very much before its time, & everything about the game is godly, it might even be my favorite.
So yeah with me it was either Twin Snakes or Snake Eater.