I used a Pioneer Premier Head Unit - with Sirius satellite tuner. I used a Pheonix Gold amp - 4 x 75W (into 4 ohms) and 1x300 (bridged) into the Sub (dual coil 2 ohm in series to 4 ohm)
Speakers: I used MBQuart 4" two-way in the dash, MBQuart 5.25" two-way in rear deck, and CL-5 5.25" midrange in the door. The doors and front speakers are wired in parallel (makes 2 ohm).
Sub is a 10" Kicker.
I used Dynamat Extreme almost everwhere, and switched to Cascade soundproofing for the rest.
My goal was great sound and yet have it look stock. Only thing you notice is a different head unit (but it's subtle and still looks classy), and the cutout in the first aid kit. However, since it's just a port from the trunk - it looks small and doesn't bely the sub under it.
Here are some pics:
Door with the 5.25" mounted in it.
Trunk showing Amp and Sub:
The silver brackets are holding on the sub grill but more importantly - they are about 1/4" above the sub - so if I do have to put something heavy in the trunk - it's not resting on the sub itself.
Head Unit:
Back deck - first aid kit cutout for trunk sub
Beck Deck - under the first aid kit