Hmm..tough decision....Let's see, Snake Eater- was the best looking, had the best bosses {both from a character standpoint and challenge}, introduced many new and cool gameplay elements, had cool characters in their prime from the earlier games, had a followable and semi logical story, and had the coolest weapons. On the flip side, Snake Eater had a really horrible camera scheme which wasn't helped by the fact that there was no radar at all. It wasn't a problem most of the time but it did lead to some frustrating moments. I really liked MGS2 alot and that one probably had the most impact on me, but the story was just too retarded for me to ever get into. MGS is really good, just not my favorite, maybe that's because me and my friends totally over played it and VR missions.
P.S. The boss fight with "The End" is one of my favorite battles of all time, I just liked everything about it.