HDDs really don't make that much noise when they aren't reading/writing do they? What if you got a solid state drive, like
this one, that had your OS and most used documents / programs. Then your HDD could be put to sleep until you needed something on it. There's a "turn-off hard disks" settting that could come in real handy.
Here's an idea I think Joe toyed with to cool the case air: Watercool a pelt with a heatsink attached to the cold side. Place it right near the mosfets so it picks up the heat radiated by them.
But... if I wanted a silent computing experience... I would just put my PC in an adjoining room and drill a hole in my wall, then thread the VGA/PS2/USB and power button through the wall. Then who cares how loud it is, as long as I can't hear it through the wall.
Oh... but you're looking for something "elegant," aren't you?