Think it uses the BT system, but doesn't use the BT protocol and instead uses a proprietary Nike one.
Nike+ uses ANT. The devices use this ANT transmitter:
http://www.nordicsemi.com/index.cfm?obj=product&act=display&pro=78
The iPhone 3GS uses the Broadcom Bluetooth/WiFi chip with some custom firmware that also can receive ANT.
http://techon.nikkeibp.co.jp/english/NEWS_EN/20060724/119373/