My following list doesn't include PO though, I never got around to finishing PO since I was mostly borrowing it from a friend so I'm refraining from including it. GZ is also exempted since I consider as part of MGSV which isn't done yet. That said, feel I should contribute with my own list. Here's mine based on my critical views towards the games:
1- MGS3
2- MGS2
3- MGS1
4- MGS4
5- MGSPW
That isn't to say that I hate MGS4, since a lot of the characters and developments there happen to be my most favorite in the series (Ocelot most especially giving me some of my most favorite MGS moments). But I just have way too many issues with its story and overall structure of game design for it to reach any higher for me. PW is great though unlike MGS4, it's more that I think it doesn't offer much else beyond being a solid MGS game; which is to say it's a good game as it is, just not all-around amazing or ground-breaking for me. But that's the thing, being a good game that's "as it is" is sometimes not enough, and with MGS4 actually having some better moments, MGS4 gets the better edge even with all my issues with it.
That said, MGS3 is still by far my most favorite in terms story, cinematography, gameplay, and the amount of enjoyment I've had with spending time digging at every little easter egg or potential interactions with the codec. Main central cast is great too, specifically Big Boss, The Boss, Eva, Ocelot and Volgin. For me it's like MGS perfected at its core: story/characters, game design and overall choice of setting/atmospher. MGS3's execution is how I feel MGS is most suited for in terms of the decisions made in its conception and execution, and I think it will be very hard for any other games to beat its place for me even in the future. My liking for MGS2 over MGS1 is more of a conceptual one in that I really enjoyed how it deconstructs MGS1 and the notion of nostalgia. It was a good slap in the face and one that I didn't feel bothered by at all. Also I really loved how ambitious the whole narrative and concepts that were being tackled.