My list goes:
Snake Eater
MGS
Guns of the Patriots
Sons of Liberty
MG
Solid Snake.
I'm not trying to be contrary by listing the original originals but I played through them a couple of weeks ago on the HD collection. I haven't played Peace Walker all the way through yet, either.
I thought MGS4 didn't have quite enough game in it to be better than the first (which I loved), and although MGS2 has gone up in my estimations since I played though it for the 25th time (after years between playthrough 24) last week, I still think the acting and story line let it down somewhat compared to the other three before it.
MGS3 had excellent boss battles and so much to it that it has to be on top. And the first two are worth playing through if you're a fan, they take about 6 hours each if you don't know what you're doing.