The USB on my iBook sounds much, much better than the headphone out.
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If you use the headphone connection the signal has been converted from digital to analog and then amplified by the electronics inside the laptop. If you use the USB connection you are passing the digital signal to an external digital to analog converter and amplifier outside the laptop. So, which sounds better would depend on whether the DAC and amp in your laptop or the DAC and amp in your external system sound better to you.