Metal Gear Solid 2. There are some aspect in it that I've grown to not like as much as I used to, but I think it's still an excellent game, and most importantly, it's more relevant than even with its themes regarding society.
The decade had other excellent games as well. Final Fantasy X is another one that always seem to rival Metal Gear Solid 2, but other titles dear to me include Wolfenstein: Enemy Territory and Titan Quest.