Don't get me wrong. The older WD HDD's including some of the Raptors put out 12 watts on read/write cycles. I'm guessing these are the ones that made the most noise. I think the 200 gigs were notorious for it, but now I own 6 WD 200 that're relitively silent and two 36 gig Raptors that are pretty quiet too.
As for how to cool them, most of the HDD's heat comes from the bottom from the motor. If this is the case then if you cool the bottom with water then cooling the rest of the drive seems rather pointless. Same with cooling the sides making cooling the top pointless. Other then the bottem of the drive the rest of it is justa heat spreader. If you open up a HDD you'll find that theres nothing touching the sides or the top that generates any real heat.
(By the way, don't open up a drive if you want to keep using it....unless you know what you're doing.)
Although I haven't tried it myself I'd assume if you watercooled the bottom of a HDD you could insulate the rest of the drive without worry. If nothing else if you try it put a thermal prob here and there after assembly for a few minutes at a time to insure the cooling solution is working and keeping the drive under it's max operating temperature or at a temperature you are comfortable with. In addition you may want to check the drives internal thermal probe temps. I'd run defrag, antivirus or maybe create a .5-2 gig file of 1's or 1's and 0's to copy, and delete to make the drive work alittle and heat up. A Hex editor could help you with this.
Edit -
Looked around a bit and found
this .
I'm guessing the chips on this HDD are just stacking their heat on top of what the drive it's self was already producing.