The greater difference in sound quality will result not from a different miniplug to miniplug cable into the iPod's headphone jack*, but using the line level output built into the iPod's dock connector.
Some of the most popular ways:
Belkin Auto Kit for iPod
Monster iCarCharger
Sendstation PocketDock Line Out USB
And, of course, Apple's Universal Dock will do this, too, just make sure you've got some way to keep it from flying around your cabin.
*(Sorry, audiophiles. Plugging a $100 cable from headphone jack to aux will still sound like junk.)