Best - MGS3 Subsistence, and by a longshot. That ending really was something inspired.
Second best - MGS1 - a lot of technical problems (fugly graphics, bad camera, bad item management), etc... but a satisfying story.
Third best - MGS4 - A powerhouse presentation. But ok story and waaaaay too much cutscenes!
Worse - MGS2 - Most hyped game ever. Worst story ever.
But, all of them suffer from those stupid ass/retardeds guards, that really piss me off.