1. a stand-alone wired webcam allows for different angles, you can place it elsewhere, some of these cameras have auto-focus, some (such as the new Logitech cameras and a couple of Creative cameras) support HD video – none of which you can do with an integrated webcam.
2. In addition, you can use the webcam for monitoring, with services like gotocamera (http://www.gotocamera.com) or software like yawcam (http://www.yawcam.com), both of which benefit from the flexibility afforded by a wired webcam.

Yes, integrated webcams are increasingly common. But the flexibility of wired webcams is, to my mind, still undisputed.