Metal Gear Solid 1, no contest. It had the perfect mix of great innovative gameplay, memorable characters, a great story with some mighty plot twists. Coming in second would be Snake Eater. Sons of Liberty is also good but there's Rose... which brings it down a notch. I didn't like Guns of the Patriot.
From the non-MSG games, I'd choose Castlevania: Lord of Shadow, it was a solid game.
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