Mine would be MGS3: Snake Eater. It perfected the classic MGS gameplay, and the new jungle and desert scenes with the new camo gave it a whole new level of stealth to use. The story was great and made sense (fuck you MGS2), the enemies were smarter in the past, good variety in weapons and areas, and a whole lot of wierd little things to notice or do.
He threw bees, and threw bees, but it was a really good and cool fight. Did a mention he threw bees?
Guy was like predator but crazy. You couldn't see him in the jungle and had to use your best wits to track him in the trees.
Holy crap what a great fight. Hiding in the woods, step by step made this slow fight one of gaming's greatest moments. You could also kill him by sniping him after his first scene in the wheelchair, or waiting a week for him to die of old age. That's really good extra detail and the best easter eggs to be found in gaming.
FIRE FIRE HOLY CRAP THIS GUY IS CRAZY. COSMONAUT GOING DOWN ARGGGGGH
Be ready to walk a long river of dead people you killed. Probably the best bad boss fight in history. Strangely the hardest fight in the game for me because of the tricky revival sequence.
She takes your gun apart, kicks your behind any chance she gets, and lets you kill her. Some big boss.
Kidding aside, I loved MGS3, and all games are great, but this was Kojima's magnum opus.