This is the best PlayStation 3 controller right now, precisely because it's not shaped like a PS3 controller.

Power A spent a good deal of time taking what's best about the Xbox 360 controller—the most natural "traditional" controller—and bringing it to the PS3. It's called the PS3 Pro Elite, and it's only $50. You have your left analog stick up on the top left and D-Pad down on the bottom. The palm parts extend much lower, and are coated with a grippy, but breathable material, which makes a huge difference when you play games for hours on end.