The real key is using the limits of the iPhone 3GS's camera as a strength, Japanese pro photographer Koichi Mitsui tells BoingBoing: Its "simplicity keeps me devoted to only composition and the perfect photo opp".
In other words, the secret is composition, composition, composition. The one real advantage the iPhone 3GS has in this regard against past iPhones is that you can change the focal point, which lets you alter the shot in subtle ways, which is one of his tips. Also, he suggests trying some different camera apps — he likes Photo fx and CameraKit, though I'm partial to CameraBag.
Here's a couple of other awesome photos he's taken, but you can see way more at his very excellent photo blog, which gives you a view of Japan that maybe you haven't seen.