digi's suggestion is what I'd suggest first. Bungee suspension seems ideal with laptop drives in desktop cases, anyway, as you can suspend a 2.5" HD in a standard 3.5" bay. Suspending a 3.5" HD probably requires more space (5.25" bay?) or thought. Anyway, these two SPCR articles are probably most relevant:
1,
2. (You can see the range of homemade HD vibration suppression at SPCR, from foam to metal to the Magic Eraser and now to elastic suspension and rubber mounts in the rest of
their early articles.)
Or, just get a case with rubber mounts, like one of the newer Antecs (
the P150's swish in this dept).
Or just buy a quieter, smoother HD.
SPCR's reviews include vibration estimates in addition to sound measurements. Apparently the new 500GB WD isn't bad, though laptop HDs reign supreme in the first category.
I've bought some bungees but haven't gotten around to trying them yet. Only experience I've had with HD decoupling was prompted by my noisy, older WD 800JB. I screwed it to a couple of 3.5->5.25" drive rails (
to aid in heat dissipation) and then just rested it on some random erasers I had lying around (two square, soft art erasers that I halved to put on each corner). I'm not sure if it's still recommended (as in, if it's been proven to be nec'y), but I also ran a wire from the HD to the case for extra grounding, as it's no longer screwed into the case. I was surprised by the reduction idle whine. (I bought another 800JB a year later, and the new one was much quieter--so much so that I didn't bother with decoupling. The old one is in an external enclosure, used only for backup. It's even whinier up on the desk, but it's not on often enough to care.)
(Edit: This was composed a while ago and sat until now, so quite a few have already mentioned SPCR, etc.)