Inspired by Bluefronts many interesting DIY posts, I quickly drew this up, trying to bring his 'New Form Factor' setup all inside the case. The plan is missing quite a few details, but maybe someone can throw in a few ideas.
I wanted to keep it down to one fan (plus HSF) if possible. And originaly thought of having it exhaust through the front. The main problems right now would be to cool the hard drive, probably ducting the PSU and then possibly some way of filtering the whole thing.
Could possibly push back the PSU like Bluefront's Super Duct
and then place a filter there somewhere.
The box holding the 120mm fan would probably be made out of wood with rubber on the edges that touch the case, and then fixed somehow.
The inside of the box as well as the channel would be covered in sound dampening material, and some or all of the 3.5" external bays for exhaust.
The entire front bezel could also be entirely lined with sound dampening.