Does it do it under load/throttle? Any check engine light? Could be running lean/detonating from a fuel pressure issue or tuning (O2 sensor out?). If you have bad bottom end bearings you will usually have low oil pressure accompanying the knock. With the engine running, pull a spark plug lead and listen for the knock. If it persists, kill the engine and test the next cylinder by removing the plug lead and repeating the process. If the knock stops, you have found the potential problem (could be more than 1 cylinder...)