For noise, you could try an AcoustiCase. Also replace stock fans with 'silent' 120mm fans, get sidemounts for your harddrive, get a silent power supply, etc.
And if you're going to isolate it you'll need ventilation, or it will overheat.
Noise is the problem, but whatever I put it in needs to vent well. The computer already runs hot, and if you stick it in a box with normal comp ventalation, then it will overheat.
Actually you could build a good case and not worry about ventilation - as micter said use watercooling. It's fairly expensive but an arctic cooling system can get your processor down below 0 and you can just run the tubes in and out of the case through sealed openings.