There are three stages to upgrade the stock stereo, in my opinion, with increasing price tags.
Replace the H/U. This will send a little more power to the speakers, and offer some EQ tuning.
Option 1 + Subwoofer. This will allow your speakers to focus on the mids/highs, and allow the subwoofer to take care of the lows.
Option 2 + 6.5" components (front). Depending on your choices, you can pick up a 4-channel amp to power both the speakers and the subwoofer (bridge channel 3/4). Leaving the rear speakers stock (and powered by the H/U), you're not messing with your staging.
Any of the three options can benefit from the use of sound deadening. Rick from RAAMaudio did a nice writeup on Nasioc about deadening:
STI sound deadening, new tutorial - NASIOC
Sound Deadener Showdown outlines your options:
Sound Deadener Showdown - Your Source for Sound Deadening Products and Information