I think if you dropped a flat (3 1/4" depth) Sub on the deck - you'd loose a lot of sound to the 'atmosphere' given the position so high and far back.
Doing it right - you'd probably need to go with dual-subs. The advantage of laying them flat though, is that you could likely go with two 12" units. That would definately bump!
These 12" Pioneers would probably sound pretty good:
http://www.pioneerelectronics.ca/POCEN/Products/Car+Audio+Video/Subwoofers/Shallow+Series/TS-SW3041D
Rick's right though - engine access would likely be tough. Maybe one could velcro the whole box for easy removal.
This is another really cool option.
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