Bangraman,
I agree with the sentiment that eliminating noise from your PC would be a wise start. In particular, I would go for a fanless, diskless desktop with a storage server located elsewhere. I have a like this and am very pleased. A good place to search for fanless machines would be here:
http://www.mini-itx.com/ They have products that should help you design & implement a fanless,diskless thin client. For a storage server, I would recommend implementing a RAID5 or RAID6 solution. Most people either (a) shudder in fear of the word RAID followed by a number != (0,1) or (b) just ignore the suggestion of a RAID5/6 solution as they think they don't need one.
For starters, I will say that having a centralized storage solution can really cut down on the everyday hassles of getting to your files if you work from a number of machines and that are perhaps geographically seperated as well. Steps to getting a nice storage server:
(1) get decent PC + (Areca,3Ware) hardware RAID card + 4,8, or more hard drives to your liking that are at the current sweet spot in pricing or just above it. Currently that is at 300GB. I have a nice XLS I update regularly of the $/GB, you too can make one too in a jiffy to find the sweet spot.
(2) Install your favorite linux distro. Why linux? Well, traditionally they have the broadest support for whatever hardware RAID card you might choose. Also, the price is right
(3) if you would like to remotely access your server from remote location, setup sshd (the SSH daemon), make sure you don't use idiotic passwords, don't allow remote root login (you can always 'su' after login), forward the port on your gateway/firewall, get a dyndns account setup, and tell your router/firewall to update the dyndns info whenever its external IP address changes
(4) setup some form of thin client support on your server to remote boot your Mini-ITX fanless box over the network. Personal favorite is the Linux Terminal Server Project, but there are others out there.
(5) Enjoy the sound of silence!
Hope this helps.
Lance