When I had my subwoofer installed, I asked the guy what the next step would be to improve the sound system in the car. He was a really strong advocate for installing sound dampening mat in the doors and elsewhere in the car ( such as Dynamat
http://www.dynamat.com/) , and claimed that while you could install upgraded speakers they'd not really sound much better in the car than stock equipment due to road noise. And it's the road noise that your stereo has to compete against in sound reproduction, thereby reducing the overall quality and experience. He stated that by installing mats even in just the doors, you'd lower the road noise in the car substantially, and therefore hear more from your stereo as is, and it would naturally sound better because of it. He made a compelling argument, and it was his assertion that the head unit, and at least the FRONT speakers / tweeters were substantial enough on their own, that sound mats would improve everything in the car as much if not more than new speakers. (The ones in the back doors, however, are kinda crappy).
Of course, he was also trying to sell me on the product since he is a dealer, but the demonstrators he had there were impressive.
I know there have been others on the boards here who have installed sound mats in their Scions. Perhaps they could weigh in on before / after in regards to stereo sound quality in their boxes.