I've been doing car audio for about 15 years.  Check out sonicelectronix, vminnovations, and audiosavings.  For a cheap upgrade go with a good set of pioneer, kenwood, or any other name brand coaxials, for a little more dough and better sound go with some components.  As far as headunit, I have a JVC KD-R900.  Has 1/8 inch in, two usb, direct ipod, bluetooth, and a bunch of other goodies.  I hook up a usb hard drive to it and have my library of tunes.