Mids in the doors, subs in the back
I have 4" speakers mounted in the doors under the wing windows. I made a point to find ones with a low enough profile that the stock window cranks don't interfere. I've changed them a few times over the years; and have had three different pair in there -they aren't too hard to find.
This puts the mid/high drivers in a pretty good location for proper sound field. The ones I have in there currently have a coaxial tweeter that can be aimed.
For bass, I made a cabinet with two 6" woofers and an amp. It fits behind the passenger seat and extends from the right edge of the driver's seat to the right edge of the passenger seat, from the floor (fitted over the center hump) to the edge of the tray under the back window.
I've been pretty happy with the set up and I get very good sound (much better than I was expecting from just a pair of 6" subwoofers) but I lose a little passenger legroom. (the cabinet tapers; it's wider at the bottom).
At the moment I need to either repaint it or cover it in carpet, and my wife would like a little more legroom so I've been looking at options.
I am pretty confident that this:
http://www.crutchfield.com/p_113KSCSW10/Kenwood-KSC-SW10.html?tp=114
will fit in the center of the car between the seats (vertically mounted against the back wall). I haven't gotten around to it yet, but I've planned to mock it up with a cardboard box and see. My current box is almost that thick in the middle, and it doesn't come anywhere close to getting in the way of my elbow when I'm shifting.