I built mine previously out of an Atom ITX board. Very low power. But after that fried, due to overheating, I now have an AM2 system. (specs in sig) I am planning to upgrade that to AM3 soon. DDR3 is less expensive and more available than DDR2.
Well, you can run any Linux distro off a pen drive. I use Ubuntu Desktop on my server. After FreeNAS didn't do what I wanted. I did previously run Windows 7 on it, but that wastes too much processing power and resources. Try out different Linux distros, see what you like. (distrowatch.com
) Use VirtualBox
Yes, you need it to be the same size, or very similar. Otherwise, you are loosing that extra space. Actually, you can use any drive for power efficiency as long as you set it to speed down when not in use. But yes, WD Greens are nice as well. I have 2 Blues and a Black on my server. Though I set them to speed down. IIRC, it is not mandatory to have two drives of the same model, but it is recommended.
Actually, AMD is much more efficent, IMO. They have Cool n Quiet. Which will clock down the CPU on the fly, using less electricity. Also, AMD will give you much more juice than the Atom can even try. If you, in the future, want to do a little more with it than a file server, AMD is an excellent choice as far as price per performance goes.
Hope that helps ya!