You have to spend the time to isolate the rattle. It can be cause by thin sheetmetal (common in Hondas) or things hitting against each other.

If it is thin sheetmetal, putting a sound deadener like Dynamat will help. Although you have to know where to put it. And there are also tons of alternatives out there that can be cheaper. To isolate the rattle, I find that using a test tone CD helps. That way the subwoofer will be playing a constant tone that will cause the rattle, and the freqs from the tweets and mids wont distract you from finding the rattle. You can DL these test tones online.

If you have two things hitting against each other, put something between them.