Just adding my two cents. I too have been plagued eternally by the S13 hatch rattle. =( I have a pair of JL 10s in a sealed box pushed by a Phoenix Gold amp, they make some seriously bangin' noise. Unfortunately so does the hatch when it's closed.
My particular rattling problem seems to be coming from the passenger side hatch frame, halfway up. My hatch window was shattered a few months ago and I'm worried that the glass place didn't put it back in right, or maybe they left some pieces or something in there. Argh.
Another thing that seems to rattle is ball bearings in the rear seatbelt assemblies, though those things are impossible to get apart so forget it. Plus, I don't know what you're talking about, I've had 5 people in my 240, and I'm 6'2!

I've also had sex in the back seat on more than one occasion. It's quite capable for a sporty hatchback.
I've also considered the Dynamatting and custom enclosure building, but it's just too much money/trouble right now. And I don't like the idea of pointing my subs forward or putting them in the back seat. Too weird and too ghetto. ;D
Let me know if you find a magic cure though. I like Masticating's suggestion with the tire well, but then what if I have a flat? =(