MGS3 was a fucking masterpiece. I was too young (11-12) when I first played MGS2 so a lot of its concepts were lost on me. Looking back, its funny how the whole 'control the digital flow of information' theme has played out in real life somewhat, considering the snowden leaks and such. Kojima was way ahead of his time.
MGS1's end was equally good. The fight with rex, Gray Fox jumping in and dying, fist fight with liquid on top of Rex, the jeep chase, considering that game was released in 1998. Sometimes I think of how the press AA'd MGS1 and 3 and think to myself, bitches, go fuck