The standard-fit speakers in most cars are constructed from the cheapest materials possible. I'd recommend trying better-quality speakers of the same size, which can fit into the same place in your car.
Look after your CDs, too - cleaner discs play with fewer problems, and tend to sound better.
If you're an iPod user, store your digital music using the least digital compression possible: I'd recommend 256kbps (kilobits per second).
Top Tip Don't spend a fortune by forking out on a car manufacturer's stereo option upgrades - you will be able to get better aftermarket equipment for your vehicle at a much better price.