It seems our systems are VERY similar. I too use Western Digital SE Hd's. I too am using an Antec case, be it a SX1030B series. (sold under the name Chieftec here)

I just couldn't resist, and this is what I've done : I've drilled out the supporting mechanism of the drive bay, and thus cleared a lot of room in the bottom of my PC. This way I can just let the harddisk bay rest on the carpet on the bottom of the PC. The fan on the drive bay still works since it can draw its air from the hole in the bottom of the front panel.

This works remakebly well. Of course, this way my harddisks (still screwed in the drive bay) are not fastened to anything in the case. But since I NEVER move my case this is not a problem.

Leaving the harddisk in the bay is not an option. It's a VERY thight fit and it would always pass the vibrations through somehow. It's simply not possible to seal every piece of iron of the case off from the harddisk bay. I've tried. The way I've ended up doing it was by far the easiest solution.

My video card now is an Asus Gforce3 Ti200. The fan on that one was REALLY noisy (possibly the noisiest one of the entire system). The really bad thing about it is that it uses ONE big heatsink (in an odd shape) to cover both the GPU and the Dram chips. (see here). So I unscrewed the small fan an put a new one on top of it (this one, the one on top). I just couldn't fasten it to the card since the fan that comes with the card is is not as thick as the new one, so I couldn't use the screws that came with it. If finally atached it with four rubber bands that I attached to the VGA card itself. This works pretty well. The fan gets held firmly where it should be held. The temperature rises no more than 46°C, a very acceptable temperature I would think. (I can check this real time with the Macpower digidoc5 unit I purchased)

BTW, anyone know the max operating temperature of a Gforce3 Chip?

This Macpower unit is really great! It show the temperature of 8 different temperature sensors that can be placed inside the case. I placed one on my VGA card, one on each HD and I let one floating in the case.
The average temperature of my HD's is now 28°C, the case ambient temerature 31°C and the VGA card runs up to 46°C. The Zalman cooler on my CPU makes sure my CPU never warms up above 35°C.

So in my case I now have :
* four 80mm case fans (two on the back of the case, one on drive bay and one above my CPU cooler). All of these fans are turned to half speed ("silent mode") with Zalman's Fan Mate 1 RPM controllers.
* one 40mm 12dB fan (on VGA card)
* The standard case PSU itself - turned out very quiet in the end (I'll return that Q technology PSU and save myself $120)

So in the end the total cost was :

Four Zalman fan mate RPM controllers @ 10$/piece
Three 80mm fans @ $15/piece
One 40mm fan : $16
One Zalman CPU cooler : $40
Sound absorbing mats : $65
Total of +/- $200

I can now hardly hear my PC running. The window in this room is open, and the ambient noise of birds chirping is actually louder that the noise produced by my PC. Now THIS was what I was looking for!

So I'll re-word my previous statement :
Would I do it again? YOU BET! The difference (now) is amazing ! For $200 I now have a system that's about as quiet as my i386 was ten years ago (you know, when the only thing in your pc that contained a fan was the PSU)