I spent two weeks searching about for a brick-n-mortar to still have an old copy of 'Subsistance' in stock (eventually found a viable online seller through Amazon, but I wasn't going to go the eBay route if I could avoid it), so I couldn't in my right mind just tack my vote on to the 'Snake Eater' pile...
MGS3 had the most grounded story of the post-PS1 MGS crowd, and the gameplay improvements immediately place it above MGS1. Sure, MGS4's story is, to coin the phrase of a close friend, "pure japanime garbage", but it was most unintelligible where you have to deal with MGS2's psychosexual ramblings... which, to me, makes it the real reason the series gets such a bad rap from gamers and critics the world 'round.
My ranking:
MGS3: Subsistence
MGS: Twin Snakes
MGS3: Snake Eater
MGS: Integral (lowered due to limited access here in the US)
Metal Gear Solid
MGS4: Guns of the Patriots
MGS2: Substance
MGS2: Sons of Liberty
*Please note: In nearly all cases, the secondary "special" releases will overtake the original release, and possibly the next original release above it.
I, for one, am waiting impatiently to see if the HD rerelease rumors are true... especially if the refinements of the later titles are to be retrofitted to the earlier games on the disk, or at least use the superior special edition releases in the compilation.