I will probably be the only person to say this but

1) MGS2 - Thats right. I said it. I thought the actual gameplay and level design still stand as the best in the series. The story is a bit weird but I dig it. It is close between this and MGS but I feel the gameplay and level design wins out. On repeated playthroughs, it is so much fun to experiment. Plus in the Demo that came with Zone of the Enders, you could make guards die and seizure up due to blood loss! It was smurfing wicked evil...they removed this from the final game :/

2) MGS
3) MG2
4) MGS3
5) MG
6) MGS4