With the old style headsets this symptom was generally due to the handlebar slipping slightly inside the reenforcing tube that surrounds the center on most bars. The tube was glued to the bar, and eventually some of the glue would fail, allowing the two to move relative to each other as you rode and the bar flexed. In very rare cases the bar would actually slip within the tube, but in most cases the sound was harmless and would eventually go away -- appearing after a few months of use and then disappearing after a year or two. Tightening the bar clamp usually did not help. Bars without the reenforcing tube, of course, did not exhibit this behavior.
One would also occasionally get creaking of the stem within the steering tube. Also harmless, and usually quieted by slightly tightening the stem bolt.
I've never studied a threadless headset real closely, but presumably, given the number of individual components, there are all sorts of things that can slip slightly relative to each other as things flex.