The two best moments in my opinion were the ending of 3 (duh) and the song that plays when Snake was imprisoned in MGS 1. It really makes you feel sorry for the guy and what's he's going through. Those two games have a lot of "minor" greatest moments too - like the long ladder or "can love bloom on a battlefield".
If I had to choose from the other games...
MGS2 - none, no matter how much I try.
MGS4 - hard too, but the ending was good - excluding all the parts Akiba was in (actually make sentence valid that for the whole game).







