I don't think there is a "best game" ever made... but Silent Hill 2 is probably the most subtle. It's not my favorite game of all time, but if I had to hold up one example of video games as high art... I wouldn't choose Shadow of the Colossus, Journey, Zelda, Bioshock, Mass Effect, or The Last of Us. I'd choose Silent Hill 2.
Silent Hill 2 is, frankly, GENIUS. It probably has the single greatest use of symbolism in gaming, and it did it over ten years ago. Games today can barely even grasp the basics of symbolism, whereas Silent Hill 2 mastered it two generations ago. Every aspect of the games structural design is brilliant, not even Dark Souls can quite match it in terms of visual focus and subtle story telling. It's like a piece of fine poetry, with everything having its place in the overall narrative. EVERYTHING is symbolic.
When you find an important item, the game uses the item to highlight a theme of the story. You don't find the flashlight lying on the ground, for instance, like in other games. When you discover the flashlight, it's attached to a mannequin wearing your wife's clothes. When you enter the room, the camera focuses on the mannequin. The room is completely dark, but the flashlight is on, illuminating the dummy. As a result it becomes the clear visual focal point of the shot. The mannequin, of course, is hugely symbolic, as it is wearing your wife's clothes from before she died. When you remove the flashlight, a new monster is introduced, which is, itself, symbolic. The structure of the room also teaches you how to use your new flashlight. You can use it to illuminate threats you didn't realize were there. However, your light will also draw enemies toward you, so you can turn it off to avoid trouble. The level design teaches you all of this through the mechanics, and doesn't feel the need to interrupt the action through lengthy tutorials. This one little section is symbolic, but it also teaches you about gameplay mechanics. It's so genius that I have yet to see a single developer utilize its brilliance since, including team silent itself.
http://youtu.be/alR6jZhv4uU?t=5m41s
There's also the symbolism of the monsters. Every enemy is sexualized, except for Pyramid Head, who you never kill (he either leaves or kills himself). This means that, every single time you do something as trivial as kill a monster, your doing something symbolic. It's reminiscent of James's violence against his wife. The game actually utilizes gameplay to reinforce the themes of the story. People keep prattling on about gaming's "Citizen Kane" moment, when they don't realize that its already come and gone. It's Silent Hill 2, and its brilliant.