Here's a pretty good all-in-one alternative to putting in an amp, subs, and custom enclosure.
KENWOOD KSC-SW1 DUAL 6.5" POWERED ENCLOSED SUBWOOFER
It fits perfectly in the storage bin right behind the passenger side rear seats without any kind of mounting. Sits on top of the removable dividers that go in the bin and also held up by the hook for the child restraint. It doesn't move at all once you put the rear seat back up. I tested it out by doing some rapid braking and it does not bounce around at all. Also, you can tuck all the extra wiring inside the hollow cross bar for a clean install.
There is also a KENWOOD KSC-SW10 which is a later version of this powered sub. It does not have as many good reviews as the model I have but is smaller and could fit in the driver side storage bin instead.
Here are some pics: