Let's face it: both are incredible soldiers, and are uniquely talented warriors with their own special skills. But, if it ever came down to a fight - of whatever nature - Snake would come out victorious xD
I honestly can't say who would win. You really can't compare those two, as they star in completely different games. Both games are great, but they're completely different archetypes. Metal Gear Solid is based on science fiction, while Slinter Cell is based on science fact.
Still, if they made a gaem out of it I'd buy it. Good job.