sub rattles hatch
Just put a song on that rattles th back badly, turn it up some, then put it on repeat. Get in the back, and put your hand on, and press on various panels until the rattle goes away on that section. Once you've located all the rattles, take the panels off, and sound-deaden the backs of them with a few layers. you may also want to use a little foam tape between pieces that contact each other or metal. RTV silicone can work well too. It takes a while to get them all, but it can be done. Good luck! It also helps to sound deaden all the plastic as snootch said, but I've never done it. Also, around each seat belt where the plastic overlaps--sometimes rattles.
Then you go to the back. The tail lights can rattle if they aren't tight. Be sure to tighten all the plastic wing nuts on the back wall. The plastic under the hatch lid can sometimes rattle. Probably rare with a milhouse. Happens more with boxes that lay flat and fire up at the hatch.
Next, the linkage that connects your trunk lock cylinder to the lock istelf can rattle. I wound some electrical tape around mine and that helped. You could also spray some sound deadening or underbody coat on all those moving parts and it would help. Also, your licence plate and rear fascia panel can rattle. I know on camaros, the panel on back that says "camaro" rattles sometimes in severe cases. And lastly, with a milhouse, the bottom pan in the well may have a tendancy to rattle. Maybe it's the muffler, I dunno. But some spray or deadener right in the bottom of the well would not only eliminate that rattle, but also help the bass reflect even more. So those are a few I've encountered or heard of. If you quiet some of them, boy does it sound better. Hope that helps.
btw, it's that hatch piece on the pssngr side (the one with the speaker that used to be in it) that rattles, and when i press on the speaker grill it stops. when i take off the speaker grill, it doesn't stop. i can't seem to figure it out. 

