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not very, unless the sub is magnetically shielded, which most aren't, most speakers are now a days, but since the subs go on the floor, they aren't.
 
I wouldn't do it, and not just because of the magnetism in the speaker, but mostly because the subwoofer would probably cause quite a lot of vibration potentially damaging the drive either by shaking it off or, more likely, making the pickup on the HD touch/crash with the disk(s) inside and destroying the drive completely...
 
Mines been sitting on top of a sub for at least two years with no problem. The sub is also right next my old G4 PowerMac so the drives in that are probably less than 6" from the speaker magnet, again no problem.
 
It all depends on whether your subwoofer is shielded or not. Mine is, so I have a hard drive on top of it and it's just fine. I'm not sure how to tell if it's shielded besides putting it next to a TV though.
 
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