Technically, the USB systems will produce a better sound because there are fewer connections on the way to the speakers. Stereos with a USB connector let you plug in a USB key filled with MP3 files, and the stereo will use the key as an audio source, just like a CD. With an auxiliary input, you are playing the music on your MP3 player, then running its output into the stereo where it gets amplified again, as opposed to the single amplification step it goes through with the USB key. In reality, you probably won't notice a difference in audio quality because it will be minimal. You may need to adjust the volume up heavily on your MP3 player to hear it through the auxiliary jack.
I'm looking to purchase a new car stereo and use my mp3 player (non-ipod) and I see some brands offer the USB connection in the front of the stereo. So I was wondering if any of you know if the USB brings a better audio quality over an auxiliary input connection or if they're the same.